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Wang Y, Yue H, Jiang Y, Huang Q, Shen J, Hailili G, Sun Z, Zhou X, Pu Y, Song H, Yuan C, Zheng Y. Oral Microbiota Linking Associations of Dietary Factors with Recurrent Oral Ulcer. Nutrients 2024; 16:1519. [PMID: 38794756 PMCID: PMC11124033 DOI: 10.3390/nu16101519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Revised: 05/14/2024] [Accepted: 05/16/2024] [Indexed: 05/26/2024] Open
Abstract
Recurrent oral ulcer (ROU) is a prevalent and painful oral disorder with implications beyond physical symptoms, impacting quality of life and necessitating comprehensive management. Understanding the interplays between dietary factors, oral microbiota, and ROU is crucial for developing targeted interventions to improve oral and systemic health. Dietary behaviors and plant-based diet indices including the healthful plant-based diet index (hPDI) were measured based on a validated food frequency questionnaire. Saliva microbial features were profiled using 16S rRNA gene amplicon sequencing. In this cross-sectional study of 579 community-based participants (aged 22-74 years, 66.5% females), 337 participants had ROU. Participants in the highest tertile of hPDI exhibited a 43% lower prevalence of ROU (odds ratio [OR] = 0.57, 95%CI: 0.34-0.94), compared to the lowest tertile, independent of demographics, lifestyle, and major chronic diseases. Participants with ROU tended to have lower oral bacterial richness (Observed ASVs, p < 0.05) and distinct bacterial structure compared to those without ROU (PERMANOVA, p = 0.02). The relative abundances of 16 bacterial genera were associated with ROU (p-FDR < 0.20). Of these, Olsenella, TM7x, and unclassified Muribaculaceae were identified as potential mediators in the association between hPDI and ROU (all p-mediations < 0.05). This study provides evidence of the intricate interplays among dietary factors, oral microbiota, and ROU, offering insights that may inform preventive and therapeutic strategies targeting diets and oral microbiomes.
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Affiliation(s)
- Yetong Wang
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai 200438, China
| | - Haiyan Yue
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai 200438, China
| | - Yuzhou Jiang
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai 200438, China
| | - Qiumin Huang
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai 200438, China
| | - Jie Shen
- School of Public Health, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Gulisiya Hailili
- School of Public Health, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Zhonghan Sun
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai 200438, China
| | - Xiaofeng Zhou
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai 200438, China
| | - Yanni Pu
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai 200438, China
| | - Huiling Song
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai 200438, China
| | - Changzheng Yuan
- School of Public Health, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Yan Zheng
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai 200438, China
- National Clinical Research Center for Aging and Medicine, Huashan Hospital, Fudan University, Shanghai 200040, China
- Ministry of Education Key Laboratory of Public Health Safety, School of Public Health, Institute of Nutrition, Fudan University, Shanghai 200032, China
- Department of Cardiology, Shanghai Institute of Cardiovascular Disease, Zhongshan Hospital, Fudan University, 1609 Xietu Road, Shanghai 200032, China
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Gao WT, Liu JX, Wang DH, Sun HJ, Zhang XY. Melatonin reduced colon inflammation but had no effect on energy metabolism in ageing Mongolian gerbils (Meriones unguiculatus). Comp Biochem Physiol C Toxicol Pharmacol 2023; 273:109731. [PMID: 37611884 DOI: 10.1016/j.cbpc.2023.109731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 07/21/2023] [Accepted: 08/20/2023] [Indexed: 08/25/2023]
Abstract
In photoperiod-sensitive wild animals, the secretion of melatonin (MT) is modulated by external photoperiod, and MT affects inflammation and the ageing process. The beneficial effects of MT in delaying the progress of ageing have been reported in laboratory mice and rats. However, little is known about MT in wild mammals. In the current study, we investigated energy metabolism, microbial community structure and colon homeostasis in ageing Mongolian gerbils (Meriones unguiculatus) through exogenous supplementation of MT to test the hypothesis that MT has beneficial effects on gut homeostasis in ageing gerbils. Exogenous MT supplementation had no effect on energy metabolism in Mongolian gerbils but reduced the levels of circulating tumor necrosis factor-α (TNF-α), immune globulin G (IgG) and corticosterone (CORT). The increase in the level of inflammation in ageing animals was related to changes in the structure and diversity of the gut microbiota. At the genus level, the relative abundance of Prevotella, Treponema, Corynebacterium, and Sphingomonas was increased in ageing animals and decreased significantly by the treatment of MT. Christensenella and Lactobacillus were attenuated in ageing animals, and tended to be enhanced by MT treatment. Functions related to glycosphingolipid biosynthesis-ganglio series and lipopolysaccharide biosynthesis (metabolisms of cofactors, vitamins and glycan) were increased in ageing animals and decreased significantly by the treatment of MT. Our data suggest that a supplement of MT could improve colon homeostasis through changing the composition of gut microbiota and reducing inflammation in ageing gerbils.
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Affiliation(s)
- Wen-Ting Gao
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Key Laboratory of Animal Resistance Biology of Shandong Province, College of Life Science, Shandong Normal University, Jinan 250358, China; CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jin-Xiu Liu
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; School of Life Sciences, Shenyang Normal University, Shenyang 110034, China
| | - De-Hua Wang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; School of Life Sciences, Shandong University, Qingdao 266237, China; CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hai-Ji Sun
- Key Laboratory of Animal Resistance Biology of Shandong Province, College of Life Science, Shandong Normal University, Jinan 250358, China.
| | - Xue-Ying Zhang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China.
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Fassatoui M, Saffarian A, Mulet C, Jamoussi H, Gamoudi A, Ben Halima Y, Hechmi M, Abdelhak S, Abid A, Sansonetti P, Pedron T, Kefi R. Gut microbiota profile and the influence of nutritional status on bacterial distribution in diabetic and healthy Tunisian subjects. Biosci Rep 2023; 43:BSR20220803. [PMID: 37669144 PMCID: PMC10500226 DOI: 10.1042/bsr20220803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 06/01/2022] [Accepted: 06/22/2022] [Indexed: 09/07/2023] Open
Abstract
Gut microbiota plays a key role in the regulation of metabolism and immunity. We investigated the profile of gut microbiota and the impact of dietary intake on gut bacterial distribution in diabetic and healthy Tunisian subjects, aiming to identify a dysbiotic condition, hence opening the way to restore eubiosis and facilitate return to health. In the present research, we enrolled 10 type 1 diabetic (T1D), 10 type 2 diabetic (T2D) patients and 13 healthy (H) subjects. Illumina Miseq technology was used to sequence V3-V4 hypervariable regions of bacterial 16SrRNA gene. Data were analyzed referring to QIIME 2 pipeline. RStudio software was used to explore the role of nutrition in gut bacterial distribution. At the phylum level, we identified an imbalanced gut microbiota composition in diabetic patients marked by a decrease in the proportion of Firmicutes and an increase in the abundance of Bacteroidetes compared with H subjects. We observed higher amounts of Fusobacteria and a decline in the levels of TM7 phyla in T1D patients compared with H subjects. However, we revealed a decrease in the proportions of Verrucomicrobia in T2D patients compared with H subjects. At the genus level, T2D subjects were more affected by gut microbiota alteration, showing a reduction in the relative abundance of Faecalibacterium, Akkermansia, Clostridium, Blautia and Oscillibacter, whereas T1D group shows a decrease in the proportion of Blautia. The gut bacteria distribution was mainly affected by fats and carbohydrates consumption. Gut microbiota composition was altered in Tunisian diabetic patients and affected by dietary habits.
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Affiliation(s)
- Meriem Fassatoui
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Tunis, Tunisia
- University of Tunis El Manar, Campus Universitaire Farhat Hached, Tunis, Tunisia
| | - Azadeh Saffarian
- Unité de Pathogénie Microbienne Moléculaire, INSERM U1202, Institut Pasteur, Paris, France
| | - Céline Mulet
- Unité de Pathogénie Microbienne Moléculaire, INSERM U1202, Institut Pasteur, Paris, France
| | - Henda Jamoussi
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Tunis, Tunisia
- Research Unit on Obesity UR18ES01, Faculty of Medicine, University Tunis El Manar, Tunis, Tunisia
| | - Amel Gamoudi
- Department of Nutritional Diseases A. National Institute of Nutrition and Food Technology, Tunis, Tunisia
| | - Yosra Ben Halima
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Tunis, Tunisia
| | - Meriem Hechmi
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Tunis, Tunisia
- University of Carthage, National Institute of Applied Science and Technology, Tunis, Tunisia
| | - Sonia Abdelhak
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Tunis, Tunisia
- University of Tunis El Manar, Campus Universitaire Farhat Hached, Tunis, Tunisia
| | - Abdelmajid Abid
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Tunis, Tunisia
| | - Philippe J. Sansonetti
- Unité de Pathogénie Microbienne Moléculaire, INSERM U1202, Institut Pasteur, Paris, France
- Chaire de Microbiologie et Maladies Infectieuses, Collège de France, Paris, France
| | - Thierry Pedron
- Unité de Pathogénie Microbienne Moléculaire, INSERM U1202, Institut Pasteur, Paris, France
| | - Rym Kefi
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Tunis, Tunisia
- University of Tunis El Manar, Campus Universitaire Farhat Hached, Tunis, Tunisia
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Yan C, Qu H, Li X, Feng B. Holothurian Wall Hydrolysate Ameliorates Cyclophosphamide-Induced Immunocompromised Mice via Regulating Immune Response and Improving Gut Microbiota. Int J Mol Sci 2023; 24:12583. [PMID: 37628768 PMCID: PMC10454611 DOI: 10.3390/ijms241612583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 07/30/2023] [Accepted: 08/07/2023] [Indexed: 08/27/2023] Open
Abstract
Some biologically active compounds isolated from sea cucumbers stimulate the body's immune response by activating immune cells. Immune function is closely related to the integrity intestinal barrier and balanced gut microbiota. However, it is unknown whether the daily administration of holothurian wall hydrolysate (HWH) ameliorated intestinal dysbiosis and barrier injury induced by immunodeficiency. This study aimed to investigate the immunomodulatory effect and the underlying mechanism of HWH in cyclophosphamide (CTX)-induced immunocompromised mice. BALB/c mice received CTX (80 mg/kg, intraperitoneally) once a day for 3 days to induce immunodeficiency, and then they received the oral administration of HWH (80 or 240 mg/kg) or levamisole hydrochloride (LH, 40 mg/kg, positive control), respectively, once a day for 7 days. We utilized 16S rRNA sequencing for microbial composition alterations, histopathological analysis for splenic and colonic morphology, Western blotting for expressions of tight junction proteins (TJs), and quantitative real-time (qRT)-PCR for measurements of pro-inflammatory cytokines. HWH attenuated the immune organ damage induced by CTX, increased the secretions of interleukin (IL)-6, IL-1β, and tumor necrosis factor (TNF)-α, and promoted the recovery of goblet cells and the production of TJs (claudin-1, occludin, and ZO-1) in the colon of the immunocompromised mice. Moreover, HWH promoted the growth of beneficial microorganisms such as Lactobacillus, Lachnospiraceae, Christensenellaceae, and Bifidobacterium, while it suppressed the populations of Ruminococcus, Staphylococcus, and Streptococcus. These results demonstrate that HWH elicits intestinal mucosal immunity, repairs the damage to intestinal mucosal integrity, and normalizes the imbalanced intestinal microbial profiles in immunocompromised mice. It may be helpful to identify the biological activities of HWH to support its potential use in new prebiotics, immunomodulatory agents, and medical additives for intestinal repair.
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Affiliation(s)
| | | | - Xinli Li
- Department of Biotechnology, College of Basic Medical Sciences, Dalian Medical University, Dalian 116044, China; (C.Y.); (H.Q.)
| | - Bin Feng
- Department of Biotechnology, College of Basic Medical Sciences, Dalian Medical University, Dalian 116044, China; (C.Y.); (H.Q.)
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Maatouk M, Rolain JM, Bittar F. Using Genomics to Decipher the Enigmatic Properties and Survival Adaptation of Candidate Phyla Radiation. Microorganisms 2023; 11:1231. [PMID: 37317205 DOI: 10.3390/microorganisms11051231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 04/28/2023] [Accepted: 05/05/2023] [Indexed: 06/16/2023] Open
Abstract
Microbial ecology is a critical field for understanding the composition, diversity, and functions of microorganisms in various environmental and health-related processes. The discovery of Candidate Phyla Radiation (CPR) through culture-independent methods has introduced a new division of microbes characterized by a symbiotic/parasitic lifestyle, small cell size, and small genome. Despite being poorly understood, CPRs have garnered significant attention in recent years due to their widespread detection in a variety of environmental and clinical samples. These microorganisms have been found to exhibit a high degree of genetic diversity compared to other microbes. Several studies have shed light on their potential importance in global biogeochemical cycles and their impact on various human activities. In this review, we provide a systematic overview of the discovery of CPRs. We then focus on describing how the genomic characteristics of CPRs have helped them interact with and adapt to other microbes in different ecological niches. Future works should focus on discovering the metabolic capacities of CPRs and, if possible, isolating them to obtain a better understanding of these microorganisms.
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Affiliation(s)
- Mohamad Maatouk
- Aix-Marseille Université, IRD, APHM, MEPHI, 13005 Marseille, France
- IHU Méditerranée Infection, 13005 Marseille, France
| | - Jean-Marc Rolain
- Aix-Marseille Université, IRD, APHM, MEPHI, 13005 Marseille, France
- IHU Méditerranée Infection, 13005 Marseille, France
| | - Fadi Bittar
- Aix-Marseille Université, IRD, APHM, MEPHI, 13005 Marseille, France
- IHU Méditerranée Infection, 13005 Marseille, France
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Ikeuchi K, Tsutsumi T, Ishizaka A, Mizutani T, Sedohara A, Koga M, Tamaoki S, Yotsuyanagi H. Modulation of duodenal and jejunal microbiota by rifaximin in mice with CCl 4-induced liver fibrosis. Gut Pathog 2023; 15:14. [PMID: 36945059 PMCID: PMC10029291 DOI: 10.1186/s13099-023-00541-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 03/07/2023] [Indexed: 03/23/2023] Open
Abstract
BACKGROUND Rifaximin is a poorly absorbed broad-spectrum antibiotic used for hepatic encephalopathy. Although increased Lactobacillaceae and decreased Bacteroidetes abundance are characteristic of hepatic encephalopathy, rifaximin does not dramatically alter the stool microbiota. As the antimicrobial effect of rifaximin increases by micellization with bile acids, we hypothesized that rifaximin alters the microbiota in the duodenum and jejunum, where the levels of bile acids are abundant. METHODS AND RESULTS Eight-week-old BALB/c mice were injected with carbon tetrachloride (CCl4) intraperitoneally for 12 weeks to induce liver fibrosis. The mice were grouped into the control (n = 9), CCl4 (n = 13), and rifaximin group in which mice were treated with rifaximin for two weeks after CCl4 administration (n = 13). We analyzed the microbiota of the duodenum, jejunum, ileum, cecum, and stool using 16S ribosomal RNA gene analysis. The content of Lactobacillaceae, the most abundant bacterial family in the duodenum and small intestine, increased in the CCl4 group, especially in the jejunum (median 67.0% vs 87.8%, p = 0.03). Rifaximin significantly decreased Lactobacillaceae content in the duodenum (median 79.4% vs 19.0%, p = 0.006) and jejunum (median 87.8% vs 61.3%, p = 0.03), but not in the ileum, cecum, and stool. Bacteroidetes abundance tended to decrease on CCl4 administration and increased following rifaximin treatment in the duodenum and jejunum. S24_7, the most abundant family in Bacteroidetes, demonstrated a significant inverse correlation with Lactobacillaceae (duodenum, r = - 0.61, p < 0.001; jejunum, r = - 0.72, p < 0.001). In the ileum, cecum, and stool, the effect of rifaximin on the microbiota was minimal, with changes within the same phylum. The percentage of bacterial families, such as Lactobacillaceae and S24_7 in the duodenum and small intestine, did not correlate with that in the stool. CONCLUSIONS The abundance of Lactobacillaceae increased in the jejunum of mice with CCl4-induced liver fibrosis, while rifaximin significantly reduced it in the duodenum and jejunum. Thus, rifaximin possibly exerts its effect by altering the duodenal and jejunal microbiota. Furthermore, changes in the duodenal and small intestinal microbiota were not associated with that of stool, suggesting that the analysis of stool microbiota is insufficient to evaluate upper intestinal microbiota.
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Affiliation(s)
- Kazuhiko Ikeuchi
- Division of Infectious Diseases, Advanced Clinical Research Center, Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-Ku, Tokyo, 108-8639, Japan
| | - Takeya Tsutsumi
- Division of Infectious Diseases, Advanced Clinical Research Center, Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-Ku, Tokyo, 108-8639, Japan.
- Department of Infection Control and Prevention, The University of Tokyo, 7-3-1 Hongo, Bunkyo-Ku, Tokyo, 113-8655, Japan.
| | - Aya Ishizaka
- Division of Infectious Diseases, Advanced Clinical Research Center, Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-Ku, Tokyo, 108-8639, Japan
| | - Taketoshi Mizutani
- Division of Infectious Diseases, Advanced Clinical Research Center, Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-Ku, Tokyo, 108-8639, Japan
| | - Ayako Sedohara
- Division of Infectious Diseases, Advanced Clinical Research Center, Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-Ku, Tokyo, 108-8639, Japan
| | - Michiko Koga
- Division of Infectious Diseases, Advanced Clinical Research Center, Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-Ku, Tokyo, 108-8639, Japan
| | - Satoru Tamaoki
- Medical Affairs Department, ASKA Pharmaceutical Co., Ltd., 2-5-1, Shibaura, Minato-Ku, Tokyo, 108-8532, Japan
| | - Hiroshi Yotsuyanagi
- Division of Infectious Diseases, Advanced Clinical Research Center, Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-Ku, Tokyo, 108-8639, Japan
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Almeida HM, Sardeli AV, Conway J, Duggal NA, Cavaglieri CR. Comparison between frail and non-frail older adults' gut microbiota: A systematic review and meta-analysis. Ageing Res Rev 2022; 82:101773. [PMID: 36349647 DOI: 10.1016/j.arr.2022.101773] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 10/28/2022] [Accepted: 10/28/2022] [Indexed: 02/07/2023]
Abstract
BACKGROUND Emerging evidence suggests that the intestinal microbiota (IM) undergoes remodelling as we age, and this impacts the ageing trajectory and mortality in older adults. The aim was to investigate IM diversity differences between frail and non-frail older adults by meta-analysing previous studies. METHODS The protocol of this systematic review with meta-analysis was registered on PROSPERO (CRD42021276733). We searched for studies comparing IM diversity of frail and non-frail older adults indexed on PubMed, Embase, Cochrane, and Web of Science in November 2021. RESULTS We included 11 studies with 1239 participants, of which 340 were meta-analysed. Frailty was defined by a variety of criteria (i.e. Fried Scale, European Consensus on Sarcopenia). There were no differences in the meta-analyses between the frail and non-frail groups for species richness index (SMD = -0.147; 95% CI = -0.394, 0.100; p = 0.243) and species diversity index (SMD = -0.033; 95% CI = -0.315, 0.250; p = 0.820). However, we identified almost 50 differences between frail and non-frail within the relative abundance of bacteria phyla, families, genera, and species in the primary studies. CONCLUSIONS The evidence to prove that there are differences between frail and non-frail IM diversity by meta-analysis is still lacking. The present results suggest that further investigation into the role of specific bacteria, their function, and their influence on the physiopathology of frailty is needed.
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Affiliation(s)
- Helena Maia Almeida
- Gerontology Program - Faculty of Medical Sciences, UNICAMP, Campinas, SP, Brazil; Laboratory of Exercise Physiology (FISEX), University of Campinas, Campinas, Brazil
| | - Amanda V Sardeli
- Gerontology Program - Faculty of Medical Sciences, UNICAMP, Campinas, SP, Brazil; Laboratory of Exercise Physiology (FISEX), University of Campinas, Campinas, Brazil; Institute of Inflammation and Ageing, University of Birmingham, Birmingham, UK.
| | - Jessica Conway
- Institute of Inflammation and Ageing, University of Birmingham, Birmingham, UK
| | | | - Cláudia Regina Cavaglieri
- Gerontology Program - Faculty of Medical Sciences, UNICAMP, Campinas, SP, Brazil; Laboratory of Exercise Physiology (FISEX), University of Campinas, Campinas, Brazil
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Tang M, Wu Z, Li W, Shoaib M, Aqib AI, Shang R, Yang Z, Pu W. Effects of different composting methods on antibiotic-resistant bacteria, antibiotic resistance genes, and microbial diversity in dairy cattle manures. J Dairy Sci 2022; 106:257-273. [DOI: 10.3168/jds.2022-22193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 08/08/2022] [Indexed: 11/13/2022]
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Webster SE, Vos D, Rothstein TL, Holodick NE. Modulation of microbiome diversity and cytokine expression is influenced in a sex-dependent manner during aging. FRONTIERS IN MICROBIOMES 2022; 1:994464. [PMID: 37426084 PMCID: PMC10328149 DOI: 10.3389/frmbi.2022.994464] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
The microbiome and immune system have a unique interplay, which influences homeostasis within the organism. Both the microbiome and immune system play important roles in health and diseases of the aged including development of cancer, autoimmune disorders, and susceptibility to infection. Various groups have demonstrated divergent changes in the gut microbiota during aging, yet the compounding factor of biological sex within the context of aging remains incompletely understood, and little is known about the effect of housing location in the composition of gut microbiota in the context of both sex and age. To better understand the roles of sex, aging, and location in influencing the gut microbiome, we obtained normal healthy BALB/cByJ mice from a single source and aged male and female mice in two different geographical locations. The 16S rRNA was analyzed from fecal samples of these mice and cytokine levels were measured from serum.16S rRNA microbiome analysis indicated that both age and sex play a role in microbiome composition, whereas location plays a lesser role in the diversity present. Interestingly, microbiome changes occurred with alterations in serum expression of several different cytokines including IL-10 and IL-6, which were also both differentially regulated in context to sex and aging. We found both IL-10 and IL-6 play a role in the constitutive expression of pSTAT-3 in CD5+ B-1 cells, which are known to regulate the microbiome. Additionally, significant correlations were found between cytokine expression and significantly abundant microbes. Based on these results, we conclude aging mice undergo sex-associated alterations in the gut microbiome and have a distinct cytokine profile. Further, there is significant interplay between B-1 cells and the microbiome which is influenced by aging in a sex-dependent manner. Together, these results illustrate the complex interrelationship among sex, aging, immunity, housing location, and the gut microbiome.
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Affiliation(s)
- Sarah E. Webster
- Center for Immunobiology, Department of Investigative Medicine, Western Michigan University Homer Stryker M.D. School of Medicine, Kalamazoo, MI, USA
| | - Duncan Vos
- Division of Epidemiology and Biostatics, Department of Biomedical Sciences, Western Michigan University Homer Stryker M.D. School of Medicine, Kalamazoo, MI, USA
| | - Thomas L. Rothstein
- Center for Immunobiology, Department of Investigative Medicine, Western Michigan University Homer Stryker M.D. School of Medicine, Kalamazoo, MI, USA
| | - Nichol E. Holodick
- Center for Immunobiology, Department of Investigative Medicine, Western Michigan University Homer Stryker M.D. School of Medicine, Kalamazoo, MI, USA
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Insight into the Relationship between Oral Microbiota and the Inflammatory Bowel Disease. Microorganisms 2022; 10:microorganisms10091868. [PMID: 36144470 PMCID: PMC9505529 DOI: 10.3390/microorganisms10091868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 09/03/2022] [Accepted: 09/09/2022] [Indexed: 11/17/2022] Open
Abstract
Inflammatory bowel disease has been a growing concern of lots of people globally, including both adults and children. As a chronic inflammatory disease of the intestine, even though the etiology of inflammatory bowel disease is still unclear, the available evidence from clinic observations has suggested a close association with microorganisms. The oral microbiota possesses the characteristics of a large number and abundant species, second only to the intestinal microbiota in the human body; as a result, it successfully attracts the attention of researchers. The highly diverse commensal oral microbiota is not only a normal part of the oral cavity but also has a pronounced impact on the pathophysiology of general health. Numerous studies have shown the potential associations between the oral microbiota and inflammatory bowel disease. Inflammatory bowel disease can affect the composition of the oral microbiota and lead to a range of oral pathologies. In turn, there are a variety of oral microorganisms involved in the development and progression of inflammatory bowel disease, including Streptococcus spp., Fusobacterium nucleatum, Porphyromonas gingivalis, Campylobacter concisus, Klebsiella pneumoniae, Saccharibacteria (TM7), and Candida albicans. Based on the above analysis, the purpose of this review is to summarize this relationship of mutual influence and give further insight into the detection of flora as a target for the diagnosis and treatment of inflammatory bowel disease to open up a novel approach in future clinical practice.
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George SE, James J, Devereux R, Wan Y, Diamond GL, Bradham KD, Scheckel KG, Thomas DJ. Ingestion of remediated lead-contaminated soils affects the fecal microbiome of mice. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 837:155797. [PMID: 35561906 PMCID: PMC9830667 DOI: 10.1016/j.scitotenv.2022.155797] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 04/12/2022] [Accepted: 05/05/2022] [Indexed: 05/08/2023]
Abstract
The relationship between ingestion of diets amended with a Pb-contaminated soil and the composition of the fecal microbiome was examined in a mouse model. Mice consumed diets amended with a Pb-contaminated soil in its native (untreated) state or after treatment for remediation with phosphoric acid or triple superphosphate alone or in combination with iron-waste material or biosolids compost. Subacute dietary exposure of mice receiving treated soil resulted in modulation of the fecal intestinal flora, which coincided with reduced relative Pb bioavailability in the bone, blood and kidney and differences in Pb speciation compared to untreated soil. Shifts in the relative abundance of several phyla including Verrucomicrobia, Tenericutes, Firmicutes, Proteobacteria, and TM7 (Candidatus Saccharibacteria) were observed. Because the phyla persist in the presence of Pb, it is probable that they are resistant to Pb. This may enable members of the phyla to bind and limit Pb uptake in the intestine. Families Ruminococcaceae, Lachnospiraceae, Erysipelotrichaceae, Verrucomicrobiaceae, Prevotellaceae, Lactobacilaceae, and Bacteroidaceae, which have been linked to health or disease, also were modulated. This study is the first to explore the relationship between the murine fecal microbiome and ingested Pb contaminated soils treated with different remediation options designed to reduce bioavailability. Identifying commonalities in the microbiome that are correlated with more positive health outcomes may serve as biomarkers to assist in the selection of remediation approaches that are more effective and pose less risk.
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Affiliation(s)
- S Elizabeth George
- Center for Environmental Measurement & Modeling, Gulf Ecosystem Measurement & Modeling Division, U.S. Environmental Protection Agency, Office of Research & Development, Gulf Breeze, FL 32561, United States.
| | - Joseph James
- Center for Environmental Measurement & Modeling, Gulf Ecosystem Measurement & Modeling Division, U.S. Environmental Protection Agency, Office of Research & Development, Gulf Breeze, FL 32561, United States
| | - Richard Devereux
- Center for Environmental Measurement & Modeling, Gulf Ecosystem Measurement & Modeling Division, U.S. Environmental Protection Agency, Office of Research & Development, Gulf Breeze, FL 32561, United States
| | - Yongshan Wan
- Center for Environmental Measurement & Modeling, Gulf Ecosystem Measurement & Modeling Division, U.S. Environmental Protection Agency, Office of Research & Development, Gulf Breeze, FL 32561, United States
| | - Gary L Diamond
- SRC, Inc., North Syracuse, New York 13212, United States
| | - Karen D Bradham
- Center for Environmental Measurement & Modeling, Watershed & Ecosystem Characterization Division, U.S. Environmental Protection Agency, Office of Research & Development, Research Triangle Park, NC 27711, United States
| | - Kirk G Scheckel
- Center for Environmental Solutions and Emergency Response, Land Remediation & Technology Division, U.S. Environmental Protection Agency, Office of Research & Development, Cincinnati, OH 45224, United States
| | - David J Thomas
- Center for Computational Toxicology & Exposure, Chemical Characterization & Exposure Division, U.S. Environmental Protection Agency, Office of Research & Development, Research Triangle Park, NC 27711, United States
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12
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Duan H, Li J, Yu L, Fan L. The road ahead of dietary restriction on anti-aging: focusing on personalized nutrition. Crit Rev Food Sci Nutr 2022; 64:891-908. [PMID: 35950606 DOI: 10.1080/10408398.2022.2110034] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Dietary restriction (DR), including caloric restriction (CR), intermittent fasting (IF), and restriction of specific food compositions, can delay aging, and the main mechanisms include regulation of nutrient-sensing pathways and gut microbiota. However, the effects of DR regimens on longevity remain controversial, as some studies have demonstrated that IF, rather than CR or diet composition, influences longevity, while other studies have shown that the restricted-carbohydrate or -protein diets, rather than CR, determine health and longevity. Many factors, including DR-related factors (carbohydrate or protein composition, degree and duration of DR), and individual differences (health status, sex, genotype, and age of starting DR), would be used to explain the controversial anti-aging effects of DR, thus highlighting the necessity of precise DR intervention for anti-aging. Personalized DR intervention in humans is challenging because of the lack of accurate aging molecular biomarkers and vast individual variability. Using machine learning to build a predictive model based on the data set of clinical features, gut microbiome and metabolome, may be a good method to achieve precise DR intervention. Therefore, this review analyzed the anti-aging effects of various DR regimens, summarized their mechanisms and influencing factors, and proposed a future research direction for achieving personalized DR regimens for slowing aging.
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Affiliation(s)
- Hui Duan
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
- School of Food Science and Technology, Jiangnan University, Wuxi, China
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, China
| | - Jinwei Li
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
- School of Food Science and Technology, Jiangnan University, Wuxi, China
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, China
| | - Leilei Yu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
- School of Food Science and Technology, Jiangnan University, Wuxi, China
- International Joint Research Laboratory for Probiotics at, Jiangnan University, Wuxi, China
| | - Liuping Fan
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
- School of Food Science and Technology, Jiangnan University, Wuxi, China
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, China
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13
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Sha Y, Wu H, Guo Y, Liu X, Mo Y, Yang Q, Wei S, Long K, Lu D, Xia Y, Zheng W, Su Z, Wei X. Effects of iodoacetic acid drinking water disinfection byproduct on the gut microbiota and its metabolism in rats. J Environ Sci (China) 2022; 117:91-104. [PMID: 35725093 DOI: 10.1016/j.jes.2022.02.048] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 02/12/2022] [Accepted: 02/20/2022] [Indexed: 06/15/2023]
Abstract
Iodoacetic acid (IAA) is an unregulated disinfection byproduct in drinking water and has been shown to exert cytotoxicity, genotoxicity, tumorigenicity, and reproductive and developmental toxicity. However, the effects of IAA on gut microbiota and its metabolism are still unknown, especially the association between gut microbiota and the metabolism and toxicity of IAA. In this study, female and male Sprague-Dawley rats were exposed to IAA at 0 and 16 mg/kg bw/day daily for 8 weeks by oral gavage. Results of 16S rRNA gene sequencing showed that IAA could alter the diversity, relative abundance and function of gut microbiota in female and male rats. IAA also increased the abundance of genes related to steroid hormone biosynthesis in the gut microbiota of male rats. Moreover, metabolomics profiling revealed that IAA could significantly disturb 6 and 13 metabolites in the feces of female and male rats, respectively. In female rats, the level of androstanediol increased in the IAA treatment group. These results were consistent with our previous findings, where IAA was identified as an androgen disruptor. Additionally, the perturbed gut microbiota and altered metabolites were correlated with each other. The results of this study indicated that IAA could disturb gut microbiota and its metabolism. These changes in gut microbiota and its metabolism were associated with the reproductive and developmental toxicity of IAA.
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Affiliation(s)
- Yujie Sha
- Department of Occupational and Environmental Health, School of Public Health, Guangxi Medical University, Nanning 530021, China
| | - Huan Wu
- Department of Occupational and Environmental Health, School of Public Health, Guangxi Medical University, Nanning 530021, China
| | - Yue Guo
- Guangxi Key Laboratory of Bioactive Molecules Research and Evaluation, Pharmaceutical College, Guangxi Medical University, Nanning 530021, China
| | - Xi Liu
- Guangxi Key Laboratory of Bioactive Molecules Research and Evaluation, Pharmaceutical College, Guangxi Medical University, Nanning 530021, China
| | - Yan Mo
- Department of Occupational and Environmental Health, School of Public Health, Guangxi Medical University, Nanning 530021, China
| | - Qiyuan Yang
- Department of Occupational and Environmental Health, School of Public Health, Guangxi Medical University, Nanning 530021, China
| | - Shumao Wei
- Department of Occupational and Environmental Health, School of Public Health, Guangxi Medical University, Nanning 530021, China
| | - Kunling Long
- Department of Occupational and Environmental Health, School of Public Health, Guangxi Medical University, Nanning 530021, China
| | - Du Lu
- Department of Occupational and Environmental Health, School of Public Health, Guangxi Medical University, Nanning 530021, China
| | - Ying Xia
- Department of Occupational and Environmental Health, School of Public Health, Guangxi Medical University, Nanning 530021, China
| | - Weiwei Zheng
- Key Laboratory of the Public Health Safety, Ministry of Education, Department of Environmental Health, School of Public Health, Fudan University, Shanghai 200032, China
| | - Zhiheng Su
- Guangxi Key Laboratory of Bioactive Molecules Research and Evaluation, Pharmaceutical College, Guangxi Medical University, Nanning 530021, China.
| | - Xiao Wei
- Department of Occupational and Environmental Health, School of Public Health, Guangxi Medical University, Nanning 530021, China; Key Laboratory of Longevity and Aging-related Diseases of Chinese Ministry of Education, Guangxi Medical University, Nanning 530021, China; Guangxi Colleges and Universities Key Laboratory of Prevention and Control of Highly Prevalent Diseases, School of Public Health, Guangxi Medical University, Nanning 530021, China; Guangxi Key Laboratory of Environment and Health Research, Guangxi Medical University, Nanning 530021, China.
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14
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Li S, Guo R, Zhang Y, Li P, Chen F, Wang X, Li J, Jie Z, Lv Q, Jin H, Wang G, Yan Q. A catalog of 48,425 nonredundant viruses from oral metagenomes expands the horizon of the human oral virome. iScience 2022; 25:104418. [PMID: 35663034 PMCID: PMC9160773 DOI: 10.1016/j.isci.2022.104418] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 03/26/2022] [Accepted: 05/12/2022] [Indexed: 12/18/2022] Open
Abstract
The human oral cavity is a hotspot of numerous, mostly unexplored, viruses that are important for maintaining oral health and microbiome homeostasis. Here, we analyzed 2,792 publicly available oral metagenomes and proposed the Oral Virus Database (OVD) comprising 48,425 nonredundant viral genomes (≥5 kbp). The OVD catalog substantially expanded the known phylogenetic diversity and host specificity of oral viruses, allowing for enhanced delineation of some underrepresented groups such as the predicted Saccharibacteria phages and jumbo viruses. Comparisons of the viral diversity and abundance of different oral cavity habitats suggested strong niche specialization of viromes within individuals. The virome variations in relation to host geography and properties were further uncovered, especially the age-dependent viral compositional signatures in saliva. Overall, the viral genome catalog describes the architecture and variability of the human oral virome, while offering new resources and insights for current and future studies. The Oral Virus Database comprises 48,425 viral genomes from 2,792 oral metagenomes Novel Saccharibacteria phages and jumbo viruses are ubiquitously distributed Oral virome shows a high degree of spatial variability Salivary virome exhibits a characteristic age-dependent pattern
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Affiliation(s)
- Shenghui Li
- Department of Microbiology, College of Basic Medical Sciences, Dalian Medical University, Dalian 116044, China.,Puensum Genetech Institute, Wuhan 430076, China.,Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing 100083, China
| | - Ruochun Guo
- Puensum Genetech Institute, Wuhan 430076, China
| | - Yue Zhang
- Puensum Genetech Institute, Wuhan 430076, China
| | - Peng Li
- Puensum Genetech Institute, Wuhan 430076, China
| | - Fang Chen
- Department of Microbiology, College of Basic Medical Sciences, Dalian Medical University, Dalian 116044, China
| | - Xifan Wang
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing 100083, China.,Department of Obstetrics and Gynecology, Columbia University, New York, NY 10032, USA
| | - Jing Li
- Department of Rheumatology and Immunology, Peking University People's Hospital, Beijing 100044, China
| | - Zhuye Jie
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Qingbo Lv
- Puensum Genetech Institute, Wuhan 430076, China
| | - Hao Jin
- Puensum Genetech Institute, Wuhan 430076, China.,College of Food Science and Engineering, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Guangyang Wang
- Department of Microbiology, College of Basic Medical Sciences, Dalian Medical University, Dalian 116044, China
| | - Qiulong Yan
- Department of Microbiology, College of Basic Medical Sciences, Dalian Medical University, Dalian 116044, China
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15
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Intestinal Microecology of Mice Exposed to TiO 2 Nanoparticles and Bisphenol A. Foods 2022; 11:foods11121696. [PMID: 35741895 PMCID: PMC9222895 DOI: 10.3390/foods11121696] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 05/30/2022] [Accepted: 06/05/2022] [Indexed: 02/01/2023] Open
Abstract
Exposure to titanium dioxide nanoparticles (TiO2 NPs) and bisphenol A (BPA) is ubiquitous, especially through dietary and other environmental pathways. In the present study, adult C57BL/6J mice were exposed to TiO2 NPs (100 mg/kg), BPA (0, 5, and 50 mg/kg), or their binary mixtures for 13 weeks. The 16S rDNA amplification sequence analysis revealed that co-exposure to TiO2 NPs and BPA altered the intestinal microbiota; however, this alteration was mainly caused by TiO2 NPs. Faecal metabolomics analysis revealed that 28 metabolites and 3 metabolic pathways were altered in the co-exposed group. This study is the first to reveal the combined effects of TiO2 NPs and BPA on the mammalian gut microbial community and metabolism dynamics, which is of great value to human health. The coexistence of TiO2 NPs and BPA in the gut poses a potential health risk due to their interaction with the gut microbiota.
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16
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Candidate Phyla Radiation, an Underappreciated Division of the Human Microbiome, and Its Impact on Health and Disease. Clin Microbiol Rev 2022; 35:e0014021. [PMID: 35658516 DOI: 10.1128/cmr.00140-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Candidate phyla radiation (CPR) is an emerging division of the bacterial domain within the human microbiota. Still poorly known, these microorganisms were first described in the environment in 1981 as "ultramicrobacteria" with a cell volume under 0.1 μm3 and were first associated with the human oral microbiota in 2007. The evolution of technology has been paramount for the study of CPR within the human microbiota. In fact, since these ultramicrobacteria have yet to be axenically cultured despite ongoing efforts, progress in imaging technology has allowed their observation and morphological description. Although their genomic abilities and taxonomy are still being studied, great strides have been made regarding their taxonomic classification, as well as their lifestyle. In addition, advancements in next-generation sequencing and the continued development of bioinformatics tools have allowed their detection as commensals in different human habitats, including the oral cavity and gastrointestinal and genital tracts, thus highlighting CPR as a nonnegligible part of the human microbiota with an impact on physiological settings. Conversely, several pathologies present dysbiosis affecting CPR levels, including inflammatory, mucosal, and infectious diseases. In this exhaustive review of the literature, we provide a historical perspective on the study of CPR, an overview of the methods available to study these organisms and a description of their taxonomy and lifestyle. In addition, their distribution in the human microbiome is presented in both homeostatic and dysbiotic settings. Future efforts should focus on developing cocultures and, if possible, axenic cultures to obtain isolates and therefore genomes that would provide a better understanding of these ultramicrobacteria, the importance of which in the human microbiome is undeniable.
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17
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New Beta-lactamases in Candidate Phyla Radiation: Owning Pleiotropic Enzymes Is a Smart Paradigm for Microorganisms with a Reduced Genome. Int J Mol Sci 2022; 23:ijms23105446. [PMID: 35628255 PMCID: PMC9145738 DOI: 10.3390/ijms23105446] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 05/09/2022] [Accepted: 05/10/2022] [Indexed: 01/08/2023] Open
Abstract
The increased exploitation of microbial sequencing methods has shed light on the high diversity of new microorganisms named Candidate Phyla Radiation (CPR). CPR are mainly detected via 16S rRNA/metabarcoding analyses or metagenomics and are found to be abundant in all environments and present in different human microbiomes. These microbes, characterized by their symbiotic/epiparasitic lifestyle with bacteria, are directly exposed to competition with other microorganisms sharing the same ecological niche. Recently, a rich repertoire of enzymes with antibiotic resistance activity has been found in CPR genomes by using an in silico adapted screening strategy. This reservoir has shown a high prevalence of putative beta-lactamase-encoding genes. We expressed and purified five putative beta-lactamase sequences having the essential domains and functional motifs from class A and class B beta-lactamase. Their enzymatic activities were tested against various beta-lactam substrates using liquid chromatography-mass spectrometry (LC-MS) and showed some beta-lactamase activity even in the presence of a beta-lactamase inhibitor. In addition, ribonuclease activity was demonstrated against RNA that was not inhibited by sulbactam and EDTA. None of these proteins could degrade single- and double-stranded-DNA. This study is the first to express and test putative CPR beta-lactamase protein sequences in vitro. Our findings highlight that the reduced genomes of CPR members harbor sequences encoding for beta-lactamases known to be multifunction hydrolase enzymes.
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18
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Li M, Zhao X, Xie J, Tong X, Shan J, Shi M, Wang G, Ye W, Liu Y, Unger BH, Cheng Y, Zhang W, Wu N, Xia XQ. Dietary Inclusion of Seabuckthorn (Hippophae rhamnoides) Mitigates Foodborne Enteritis in Zebrafish Through the Gut-Liver Immune Axis. Front Physiol 2022; 13:831226. [PMID: 35464096 PMCID: PMC9019508 DOI: 10.3389/fphys.2022.831226] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 03/21/2022] [Indexed: 12/12/2022] Open
Abstract
To help prevent foodborne enteritis in aquaculture, several feed additives, such as herbal medicine, have been added to fish diets. Predictions of effective herb medicines for treating fish foodborne enteritis from key regulated DEGs (differentially expressed genes) in transcriptomic data can aid in the development of feed additives using the Traditional Chinese Medicine Integrated Database. Seabuckthorn has been assessed as a promising candidate for treating grass carp soybean-induced enteritis (SBMIE). In the present study, the SBMIE zebrafish model was used to assess seabuckthorn’s therapeutic or preventative effects. The results showed that intestinal and hepatic inflammation was reduced when seabuckthorn was added, either pathologically (improved intestinal villi morphology, less oil-drops) or growth-related (body fat deposition). Moreover, seabuckthorn may block the intestinal p53 signaling pathway, while activating the PPAR signaling pathway and fatty acid metabolism in the liver. 16S rRNA gene sequencing results also indicated a significant increase in OTU numbers and skewed overlapping with the fish meal group following the addition of seabuckthorn. Additionally, there were signs of altered gut microbiota taxa composition, particularly for reduced TM7, Sphingomonas, and Shigella, following the addition of seabuckthorn. Hindgut imaging of fluorescent immune cells in SBMIE larvae revealed the immune regulatory mechanisms at the cellular level. Seabuckthorn may significantly inhibit the inflammatory gathering of neutrophils, macrophages, and mature T cells, as well as cellular protrusions’ formation. On the other hand, in larvae, seabuckthorn inhibited the inflammatory aggregation of lck+ T cells but not immature lymphocytes, indicating that it affected intestinal adaptive immunity. Although seabuckthorn did not affect the distribution of intestinal CD4+ cells, the number of hepatic CD4+ cells were reduced in fish from the seabuckthorn supplementation group. Thus, the current data indicate that seabuckthorn may alleviate foodborne gut-liver symptoms by enhancing intestinal mucosal immunity and microbiota while simultaneously inhibiting hepatic adipose disposition, making it a potential additive for preventing fish foodborne gut-liver symptoms.
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Affiliation(s)
- Ming Li
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- College of Fisheries and Life Science, Dalian Ocean University, Dalian, China
| | - Xuyang Zhao
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- College of Fisheries and Life Science, Dalian Ocean University, Dalian, China
| | - Jiayuan Xie
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Xinyu Tong
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, China
| | - Junwei Shan
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- College of Fisheries and Life Science, Dalian Ocean University, Dalian, China
| | - Mijuan Shi
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Guangxin Wang
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Weidong Ye
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yuhang Liu
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- College of Fisheries and Life Science, Dalian Ocean University, Dalian, China
| | | | - Yingyin Cheng
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Wanting Zhang
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Nan Wu
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
- *Correspondence: Nan Wu, ; Xiao-Qin Xia,
| | - Xiao-Qin Xia
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
- *Correspondence: Nan Wu, ; Xiao-Qin Xia,
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19
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Dataset for Genome Sequencing and De Novo Assembly of the Candidate Phyla Radiation in Supragingival Plaque. THE CANADIAN JOURNAL OF INFECTIOUS DISEASES & MEDICAL MICROBIOLOGY = JOURNAL CANADIEN DES MALADIES INFECTIEUSES ET DE LA MICROBIOLOGIE MEDICALE 2022; 2022:4899824. [PMID: 35345870 PMCID: PMC8957474 DOI: 10.1155/2022/4899824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Accepted: 01/26/2022] [Indexed: 11/17/2022]
Abstract
The Candidate Phyla Radiation (CPR), as a newly discovered and difficult-to-culture bacterium, accounts for the majority of the bacterial domain, which may be related to various oral diseases, including dental caries. Restricted by laboratory culture conditions, there is limited knowledge about oral CPR. Advances in metagenomics provide a new way to study CPR through molecular biology. Here, we used metagenomic assembly and binning to reconstruct more and higher quality metagenome-assembled genomes (MAGs) of CPR from oral dental plaque. These MAGs represent novel CPR species, which differed from all known CPR organisms. Relative abundance of different CPR MAGs in the caries and caries-free group was estimated by mapping metagenomic reads to newly constructed MAGs. The relative abundance of two CPR MAGs was significantly increased in the caries group, indicating that there might be a relationship with caries activity. The detection of a large number of unclassified CPR MAGs in the dataset implies that the phylogenetic diversity of CPR is enormous. The results provide a reference value for exploring the ecological distribution and function of uncultured or difficult-to-culture microorganisms.
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20
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Ibrahim A, Maatouk M, Raoult D, Bittar F. Reverse Genomics: Design of Universal Epitope Sets to Isolate All Saccharibacteria Members from the Human Oral Cavity. Microorganisms 2022; 10:microorganisms10030602. [PMID: 35336177 PMCID: PMC8954561 DOI: 10.3390/microorganisms10030602] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 03/04/2022] [Accepted: 03/08/2022] [Indexed: 12/20/2022] Open
Abstract
Microorganisms not yet cultured represent a large proportion of the microbes described to date. Progress in sequencing and metagenomic tools continues to increase microbial diversity without providing information on their physiological and pathophysiological characteristics, such as the recent discovery of enigmatic microbes belonging to Candidate Phyla Radiation (CPR). Reverse genomics is a recent technique allowing co-cultivation of a few CPR members, affiliated to the Saccharibacteria phylum, based on the analysis of their already-available genomes. Here, our aim is to designate a common system capable of cultivating any given taxon of this phylum from human samples. We managed to design, in silico, 11 common epitopes for all Saccharibacteria species recovered from the human oral cavity and which can serve as antigens via bioinformatics analyses. These sequences allow the synthesis of target antibodies, sorting Saccharibacteria spp. by flow cytometry and co-culturing them afterwards with adapted hosts. This epitope set can facilitate the cultivation of CPR in general, which in recent years has been considered a challenge for microbiologists, and subsequently contributes to better studying this new branch on the tree of life.
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Affiliation(s)
- Ahmad Ibrahim
- IHU Méditerranée Infection, 13005 Marseille, France; (A.I.); (M.M.); (D.R.)
- Aix-Marseille Université, IRD, APHM, MEPHI, 13005 Marseille, France
| | - Mohamad Maatouk
- IHU Méditerranée Infection, 13005 Marseille, France; (A.I.); (M.M.); (D.R.)
- Aix-Marseille Université, IRD, APHM, MEPHI, 13005 Marseille, France
| | - Didier Raoult
- IHU Méditerranée Infection, 13005 Marseille, France; (A.I.); (M.M.); (D.R.)
- Aix-Marseille Université, IRD, APHM, MEPHI, 13005 Marseille, France
| | - Fadi Bittar
- IHU Méditerranée Infection, 13005 Marseille, France; (A.I.); (M.M.); (D.R.)
- Aix-Marseille Université, IRD, APHM, MEPHI, 13005 Marseille, France
- Correspondence:
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21
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Noh JY, Wu CS, DeLuca JAA, Devaraj S, Jayaraman A, Alaniz RC, Tan XD, Allred CD, Sun Y. Novel Role of Ghrelin Receptor in Gut Dysbiosis and Experimental Colitis in Aging. Int J Mol Sci 2022; 23:2219. [PMID: 35216335 PMCID: PMC8875592 DOI: 10.3390/ijms23042219] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 02/13/2022] [Accepted: 02/14/2022] [Indexed: 01/25/2023] Open
Abstract
Chronic low-grade inflammation is a hallmark of aging, which is now coined as inflamm-aging. Inflamm-aging contributes to many age-associated diseases such as obesity, type 2 diabetes, cardiovascular disease, and inflammatory bowel disease (IBD). We have shown that gut hormone ghrelin, via its receptor growth hormone secretagogue receptor (GHS-R), regulates energy metabolism and inflammation in aging. Emerging evidence suggests that gut microbiome has a critical role in intestinal immunity of the host. To determine whether microbiome is an integral driving force of GHS-R mediated immune-metabolic homeostasis in aging, we assessed the gut microbiome profiles of young and old GHS-R global knockout (KO) mice. While young GHS-R KO mice showed marginal changes in Bacteroidetes and Firmicutes, aged GHS-R KO mice exhibited reduced Bacteroidetes and increased Firmicutes, featuring a disease-susceptible microbiome profile. To further study the role of GHS-R in intestinal inflammation in aging, we induced acute colitis in young and aged GHS-R KO mice using dextran sulfate sodium (DSS). The GHS-R KO mice showed more severe disease activity scores, higher proinflammatory cytokine expression, and decreased expression of tight junction markers. These results suggest that GHS-R plays an important role in microbiome homeostasis and gut inflammation during aging; GHS-R suppression exacerbates intestinal inflammation in aging and increases vulnerability to colitis. Collectively, our finding reveals for the first time that GHS-R is an important regulator of intestinal health in aging; targeting GHS-R may present a novel therapeutic strategy for prevention/treatment of aging leaky gut and inflammatory bowel disease.
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Affiliation(s)
- Ji Yeon Noh
- Department of Nutrition, Texas A&M University, College Station, TX 77843, USA; (J.Y.N.); (C.-S.W.); (J.A.A.D.); (C.D.A.)
| | - Chia-Shan Wu
- Department of Nutrition, Texas A&M University, College Station, TX 77843, USA; (J.Y.N.); (C.-S.W.); (J.A.A.D.); (C.D.A.)
| | - Jennifer A. A. DeLuca
- Department of Nutrition, Texas A&M University, College Station, TX 77843, USA; (J.Y.N.); (C.-S.W.); (J.A.A.D.); (C.D.A.)
| | - Sridevi Devaraj
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX 77030, USA;
| | - Arul Jayaraman
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX 77843, USA;
| | - Robert C. Alaniz
- Department of Microbial Pathogenesis and Immunology, Texas A&M University Health Science Center, College Station, TX 77843, USA;
| | - Xiao-Di Tan
- Department of Pediatrics, Ann & Robert H. Lurie Children’s Hospital of Chicago, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA;
| | - Clinton D. Allred
- Department of Nutrition, Texas A&M University, College Station, TX 77843, USA; (J.Y.N.); (C.-S.W.); (J.A.A.D.); (C.D.A.)
- Department of Nutrition, University of North Carolina at Greensboro, Greensboro, NC 27412, USA
| | - Yuxiang Sun
- Department of Nutrition, Texas A&M University, College Station, TX 77843, USA; (J.Y.N.); (C.-S.W.); (J.A.A.D.); (C.D.A.)
- USDA/ARS Children’s Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
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22
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Ren B, Wang L, Mulati A, Liu Y, Liu Z, Liu X. Methionine Restriction Improves Gut Barrier Function by Reshaping Diurnal Rhythms of Inflammation-Related Microbes in Aged Mice. Front Nutr 2022; 8:746592. [PMID: 35004799 PMCID: PMC8733897 DOI: 10.3389/fnut.2021.746592] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Accepted: 12/03/2021] [Indexed: 12/25/2022] Open
Abstract
Age-related gut barrier dysfunction and dysbiosis of the gut microbiome play crucial roles in human aging. Dietary methionine restriction (MR) has been reported to extend lifespan and reduce the inflammatory response; however, its protective effects on age-related gut barrier dysfunction remain unclear. Accordingly, we focus on the effects of MR on inflammation and gut function. We found a 3-month methionine-restriction reduced inflammatory factors in the serum of aged mice. Moreover, MR reduced gut permeability in aged mice and increased the levels of the tight junction proteins mRNAs, including those of occludin, claudin-1, and zona occludens-1. MR significantly reduced bacterial endotoxin lipopolysaccharide concentration in aged mice serum. By using 16s rRNA sequencing to analyze microbiome diurnal rhythmicity during 24 h, we found MR moderately recovered the cyclical fluctuations of the gut microbiome which was disrupted in aged mice, leading to time-specific enhancement of the abundance of short-chain fatty acid-producing and lifespan-promoting microbes. Moreover, MR dampened the oscillation of inflammation-related TM7-3 and Staphylococcaceae. In conclusion, the effects of MR on the gut barrier were likely related to alleviation of the oscillations of inflammation-related microbes. MR can enable nutritional intervention against age-related gut barrier dysfunction.
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Affiliation(s)
- Bo Ren
- Laboratory of Functional Chemistry and Nutrition of Food, College of Food Science and Engineering, Northwest A&F University, Yangling, China.,School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, China
| | - Luanfeng Wang
- Laboratory of Functional Chemistry and Nutrition of Food, College of Food Science and Engineering, Northwest A&F University, Yangling, China
| | - Aiziguli Mulati
- Laboratory of Functional Chemistry and Nutrition of Food, College of Food Science and Engineering, Northwest A&F University, Yangling, China
| | - Yan Liu
- Laboratory of Functional Chemistry and Nutrition of Food, College of Food Science and Engineering, Northwest A&F University, Yangling, China
| | - Zhigang Liu
- Laboratory of Functional Chemistry and Nutrition of Food, College of Food Science and Engineering, Northwest A&F University, Yangling, China
| | - Xuebo Liu
- Laboratory of Functional Chemistry and Nutrition of Food, College of Food Science and Engineering, Northwest A&F University, Yangling, China
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23
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El-Sahhar S, Varga-Weisz P. The gut microbiome in health and disease: Inflammatory bowel diseases. ADV ECOL RES 2022. [DOI: 10.1016/bs.aecr.2022.09.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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24
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Maatouk M, Ibrahim A, Rolain JM, Merhej V, Bittar F. Small and Equipped: the Rich Repertoire of Antibiotic Resistance Genes in Candidate Phyla Radiation Genomes. mSystems 2021; 6:e0089821. [PMID: 34874773 PMCID: PMC8651080 DOI: 10.1128/msystems.00898-21] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 11/10/2021] [Indexed: 11/20/2022] Open
Abstract
Microbes belonging to Candidate Phyla Radiation (CPR) have joined the tree of life as a new branch, thanks to the intensive application of metagenomics and sequencing technologies. CPR have been eventually identified by 16S rRNA analysis, and they represent more than 26% of microbial diversity. Despite their ultrasmall size, reduced genome, and metabolic pathways which mainly depend on exosymbiotic or exoparasitic relationships with the bacterial host, CPR microbes were found to be abundant in almost all environments. They can be considered survivors in highly competitive circumstances within microbial communities. However, their defense mechanisms and phenotypic characteristic remain poorly explored. Here, we conducted a thorough in silico analysis on 4,062 CPR genomes to search for antibiotic resistance (AR)-like enzymes using BLASTp and functional domain predictions against an exhaustive consensus AR database and conserved domain database (CDD), respectively. Our findings showed that a rich reservoir of divergent AR-like genes (n = 30,545 hits, mean = 7.5 hits/genome [0 to 41]) were distributed across the 13 CPR superphyla. These AR-like genes encode 89 different enzymes that are associated with 14 different chemical classes of antimicrobials. Most hits found (93.6%) were linked to glycopeptide, beta-lactam, macrolide-lincosamide-streptogramin (MLS), tetracycline, and aminoglycoside resistance. Moreover, two AR profiles were discerned for the Microgenomates group and "Candidatus Parcubacteria," which were distinct between them and differed from all other CPR superphyla. CPR cells seem to be active players during microbial competitive interactions; they are well equipped for microbial combat in different habitats, which ensures their natural survival and continued existence. IMPORTANCE To our knowledge, this study is one of the few studies that characterize the defense systems in the CPR group and describes the first repertoire of antibiotic resistance (AR) genes. The use of a BLAST approach with lenient criteria followed by a careful examination of the functional domains has yielded a variety of enzymes that mainly give three different mechanisms of action of resistance. Our genome analysis showed the existence of a rich reservoir of CPR resistome, which is associated with different antibiotic families. Moreover, this analysis revealed the hidden face of the reduced-genome CPR, particularly their weaponry with AR genes. These data suggest that CPR are competitive players in the microbial war, and they can be distinguished by specific AR profiles.
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Affiliation(s)
- Mohamad Maatouk
- Aix-Marseille Univ, IRD, APHM, MEPHI, Marseille, France
- IHU Méditerranée Infection, Marseille, France
| | - Ahmad Ibrahim
- Aix-Marseille Univ, IRD, APHM, MEPHI, Marseille, France
- IHU Méditerranée Infection, Marseille, France
| | - Jean-Marc Rolain
- Aix-Marseille Univ, IRD, APHM, MEPHI, Marseille, France
- IHU Méditerranée Infection, Marseille, France
| | - Vicky Merhej
- Aix-Marseille Univ, IRD, APHM, MEPHI, Marseille, France
- IHU Méditerranée Infection, Marseille, France
| | - Fadi Bittar
- Aix-Marseille Univ, IRD, APHM, MEPHI, Marseille, France
- IHU Méditerranée Infection, Marseille, France
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25
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Xie J, Li M, Ye W, Shan J, Zhao X, Duan Y, Liu Y, Unger BH, Cheng Y, Zhang W, Wu N, Xia XQ. Sinomenine Hydrochloride Ameliorates Fish Foodborne Enteritis via α7nAchR-Mediated Anti-Inflammatory Effect Whilst Altering Microbiota Composition. Front Immunol 2021; 12:766845. [PMID: 34887862 PMCID: PMC8650311 DOI: 10.3389/fimmu.2021.766845] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 11/02/2021] [Indexed: 02/06/2023] Open
Abstract
Foodborne intestinal inflammation is a major health and welfare issue in aquaculture. To prevent enteritis, various additives have been incorporated into the fish diet. Considering anti-inflammatory immune regulation, an effective natural compound could potentially treat or prevent intestinal inflammation. Our previous study has revealed galantamine’s effect on soybean induced enteritis (SBMIE) and has highlighted the possible role of the cholinergic anti-inflammatory pathway in the fish gut. To further activate the intestinal cholinergic related anti-inflammatory function, α7nAchR signaling was considered. In this study, sinomenine, a typical agonist of α7nAChR in mammals, was tested to treat fish foodborne enteritis via its potential anti-inflammation effect using the zebrafish foodborne enteritis model. After sinomenine’s dietary inclusion, results suggested that there was an alleviation of intestinal inflammation at a pathological level. This outcome was demonstrated through the improved morphology of intestinal villi. At a molecular level, SN suppressed inflammatory cytokines’ expression (especially for tnf-α) and upregulated anti-inflammation-related functions (indicated by expression of il-10, il-22, and foxp3a). To systematically understand sinomenine’s intestinal effect on SBMIE, transcriptomic analysis was done on the SBMIE adult fish model. DEGs (sinomenine vs soybean meal groups) were enriched in GO terms related to the negative regulation of lymphocyte/leukocyte activation and alpha-beta T cell proliferation, as well as the regulation of lymphocyte migration. The KEGG pathways for glycolysis and insulin signaling indicated metabolic adjustments of α7nAchR mediated anti-inflammatory effect. To demonstrate the immune cells’ response, in the SBMIE larva model, inflammatory gatherings of neutrophils, macrophages, and lymphocytes caused by soybean meal could be relieved significantly with the inclusion of sinomenine. This was consistent within the sinomenine group as CD4+ or Foxp3+ lymphocytes were found with a higher proportion at the base of mucosal folds, which may suggest the Treg population. Echoing, the sinomenine group’s 16s sequencing result, there were fewer enteritis-related TM7, Sphingomonas and Shigella, but more Cetobacterium, which were related to glucose metabolism. Our findings indicate that sinomenine hydrochloride could be important in the prevention of fish foodborne enteritis at both immune and microbiota levels.
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Affiliation(s)
- Jiayuan Xie
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.,College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Ming Li
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.,College of Fisheries and Life Science, Dalian Ocean University, Dalian, China
| | - Weidong Ye
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.,College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Junwei Shan
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.,College of Fisheries and Life Science, Dalian Ocean University, Dalian, China
| | - Xuyang Zhao
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.,College of Fisheries and Life Science, Dalian Ocean University, Dalian, China
| | - You Duan
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.,College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yuhang Liu
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.,College of Fisheries and Life Science, Dalian Ocean University, Dalian, China
| | | | - Yingyin Cheng
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Wanting Zhang
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Nan Wu
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.,College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Xiao-Qin Xia
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.,College of Fisheries and Life Science, Dalian Ocean University, Dalian, China
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26
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Del Chierico F, Trapani V, Petito V, Reddel S, Pietropaolo G, Graziani C, Masi L, Gasbarrini A, Putignani L, Scaldaferri F, Wolf FI. Dietary Magnesium Alleviates Experimental Murine Colitis through Modulation of Gut Microbiota. Nutrients 2021; 13:nu13124188. [PMID: 34959740 PMCID: PMC8707433 DOI: 10.3390/nu13124188] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 11/10/2021] [Accepted: 11/16/2021] [Indexed: 12/14/2022] Open
Abstract
Nutritional deficiencies are common in inflammatory bowel diseases (IBD). In patients, magnesium (Mg) deficiency is associated with disease severity, while in murine models, dietary Mg supplementation contributes to restoring mucosal function. Since Mg availability modulates key bacterial functions, including growth and virulence, we investigated whether the beneficial effects of Mg supplementation during colitis might be mediated by gut microbiota. The effects of dietary Mg modulation were assessed in a murine model of dextran sodium sulfate (DSS)-induced colitis by monitoring magnesemia, weight, and fecal consistency. Gut microbiota were analyzed by 16S-rRNA based profiling on fecal samples. Mg supplementation improved microbiota richness in colitic mice, increased abundance of Bifidobacterium and reduced Enterobacteriaceae. KEEG pathway analysis predicted an increase in biosynthetic metabolism, DNA repair and translation pathways during Mg supplementation and in the presence of colitis, while low Mg conditions favored catabolic processes. Thus, dietary Mg supplementation increases bacteria involved in intestinal health and metabolic homeostasis, and reduces bacteria involved in inflammation and associated with human diseases, such as IBD. These findings suggest that Mg supplementation may be a safe and cost-effective strategy to ameliorate disease symptoms and restore a beneficial intestinal flora in IBD patients.
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Affiliation(s)
- Federica Del Chierico
- Multimodal Laboratory Medicine Research Area, Unit of Human Microbiome, Bambino Gesù Children’s Hospital, IRCCS, 00147 Rome, Italy; (F.D.C.); (S.R.)
| | - Valentina Trapani
- Dipartimento di Medicina e Chirurgia Traslazionale, Fondazione Policlinico Universitario A. Gemelli IRCCS—Università Cattolica del Sacro Cuore, 00168 Rome, Italy; (V.T.); (V.P.); (G.P.); (C.G.); (L.M.); (A.G.)
| | - Valentina Petito
- Dipartimento di Medicina e Chirurgia Traslazionale, Fondazione Policlinico Universitario A. Gemelli IRCCS—Università Cattolica del Sacro Cuore, 00168 Rome, Italy; (V.T.); (V.P.); (G.P.); (C.G.); (L.M.); (A.G.)
| | - Sofia Reddel
- Multimodal Laboratory Medicine Research Area, Unit of Human Microbiome, Bambino Gesù Children’s Hospital, IRCCS, 00147 Rome, Italy; (F.D.C.); (S.R.)
| | - Giuseppe Pietropaolo
- Dipartimento di Medicina e Chirurgia Traslazionale, Fondazione Policlinico Universitario A. Gemelli IRCCS—Università Cattolica del Sacro Cuore, 00168 Rome, Italy; (V.T.); (V.P.); (G.P.); (C.G.); (L.M.); (A.G.)
| | - Cristina Graziani
- Dipartimento di Medicina e Chirurgia Traslazionale, Fondazione Policlinico Universitario A. Gemelli IRCCS—Università Cattolica del Sacro Cuore, 00168 Rome, Italy; (V.T.); (V.P.); (G.P.); (C.G.); (L.M.); (A.G.)
| | - Letizia Masi
- Dipartimento di Medicina e Chirurgia Traslazionale, Fondazione Policlinico Universitario A. Gemelli IRCCS—Università Cattolica del Sacro Cuore, 00168 Rome, Italy; (V.T.); (V.P.); (G.P.); (C.G.); (L.M.); (A.G.)
| | - Antonio Gasbarrini
- Dipartimento di Medicina e Chirurgia Traslazionale, Fondazione Policlinico Universitario A. Gemelli IRCCS—Università Cattolica del Sacro Cuore, 00168 Rome, Italy; (V.T.); (V.P.); (G.P.); (C.G.); (L.M.); (A.G.)
- CEMAD—IBD UNIT—Unità Operativa Complessa di Medicina Interna e Gastroenterologia, Dipartimento di Scienze Mediche e Chirurgiche, Fondazione Policlinico Universitario “A. Gemelli”, IRCCS, 00168 Rome, Italy
| | - Lorenza Putignani
- Unit of Microbiology and Diagnostic Immunology, Unit of Microbiomics and Multimodal Laboratory Medicine Research Area, Unit of Human Microbiome, Department of Diagnostic and Laboratory Medicine, Bambino Gesù Children’s Hospital, IRCCS, 00165 Rome, Italy;
| | - Franco Scaldaferri
- Dipartimento di Medicina e Chirurgia Traslazionale, Fondazione Policlinico Universitario A. Gemelli IRCCS—Università Cattolica del Sacro Cuore, 00168 Rome, Italy; (V.T.); (V.P.); (G.P.); (C.G.); (L.M.); (A.G.)
- CEMAD—IBD UNIT—Unità Operativa Complessa di Medicina Interna e Gastroenterologia, Dipartimento di Scienze Mediche e Chirurgiche, Fondazione Policlinico Universitario “A. Gemelli”, IRCCS, 00168 Rome, Italy
- Correspondence: (F.S.); (F.I.W.)
| | - Federica I. Wolf
- Dipartimento di Medicina e Chirurgia Traslazionale, Fondazione Policlinico Universitario A. Gemelli IRCCS—Università Cattolica del Sacro Cuore, 00168 Rome, Italy; (V.T.); (V.P.); (G.P.); (C.G.); (L.M.); (A.G.)
- Saint Camillus International University of Health Sciences-UniCamillus, 00131 Rome, Italy
- Correspondence: (F.S.); (F.I.W.)
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27
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Taylor HB, Vasu C. Impact of Prebiotic β-glucan Treatment at Juvenile Age on the Gut Microbiota Composition and the Eventual Type 1 Diabetes Onset in Non-obese Diabetic Mice. Front Nutr 2021; 8:769341. [PMID: 34805251 PMCID: PMC8595985 DOI: 10.3389/fnut.2021.769341] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 10/12/2021] [Indexed: 12/12/2022] Open
Abstract
Complex dietary polysaccharides such as β-glucans are widely used for their anti-inflammatory properties. We reported before that oral administration of Yeast β-glucan (YBG) in adult mice can help delay type 1 diabetes (T1D) onset and suppress gut inflammation through modulation of the structure and function of gut microbiota. Since juvenile age is characterized by profoundly changing immature gut microbiota, we examined the impact of oral treatment with YBG in non-obese diabetic (NOD) mice at this age. Juvenile mice that received daily oral administration of YBG starting at 15 days of age for 7 or 30 days were examined for changes in gut microbiota, immune characteristics, and T1D incidence. Mice that received YBG for 30 days but not 7 days, showed considerable changes in the composition and diversity of fecal microbiota as compared to controls. Predictive functional analysis, based on 16S rDNA sequences, revealed overrepresentation of glycan biosynthesis and metabolism, energy metabolism, and fatty acid biosynthesis pathways in mice that received YBG for 30 days. Immune phenotype of the colon showed skewing toward immune regulatory and Th17 cytokines with increases in IL-10, IL-17, and IL-21 and a decrease in TNF-α, although increases in some pro-inflammatory cytokines (IL-1b, IFN-γ) were observed. Most importantly, mice that received YBG treatment for 30 days showed significantly suppressed insulitis and delayed onset of hyperglycemia compared to controls. Overall, this study suggests that oral consumption of YBG beginning at pre-diabetic juvenile ages could have positive maturational changes to gut microbiota and immune functions and could result in a delay in the disease onset in those who are pre-disposed to T1D.
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Affiliation(s)
| | - Chenthamarakshan Vasu
- Department of Microbiology and Immunology, College of Medicine, Medical University of South Carolina, Charleston, SC, United States
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28
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de Maria YNLF, Aciole Barbosa D, Menegidio FB, Santos KBNH, Humberto AC, Alencar VC, Silva JFS, Costa de Oliveira R, Batista ML, Nunes LR, Jabes DL. Analysis of mouse faecal dysbiosis, during the development of cachexia, induced by transplantation with Lewis lung carcinoma cells. MICROBIOLOGY (READING, ENGLAND) 2021; 167. [PMID: 34596506 DOI: 10.1099/mic.0.001088] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Cachexia (CC) is a complex wasting syndrome that significantly affects life quality and life expectancy among cancer patients. Original studies, in which CC was induced in mouse models through inoculation with BaF and C26 tumour cells, demonstrated that CC development correlates with bacterial gut dysbiosis in these animals. In both cases, a common microbial signature was observed, based on the expansion of Enterobacteriaceae in the gut of CC animals. However, these two types of tumours induce unique microbial profiles, suggesting that different CC induction mechanisms significantly impact the outcome of gut dysbiosis. The present study sought to expand the scope of such analyses by characterizing the CC-associated dysbiosis that develops when mice are inoculated with Lewis lung carcinoma (LLC) cells, which constitutes one of the most widely employed mechanisms for CC induction. Interestingly, Enterobacteriaceae expansion is also observed in LLC-induced CC. However, the dysbiosis identified herein displays a more complex pattern, involving representatives from seven different bacterial phyla, which were consistently identified across successive levels of taxonomic hierarchy. These results are supported by a predictive analysis of gene content, which identified a series of functional/structural changes that potentially occur in the gut bacterial population of these animals, providing a complementary and alternative approach to microbiome analyses based solely on taxonomic classification.
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Affiliation(s)
- Yara N L F de Maria
- Núcleo Integrado de Biotecnologia, Universidade de Mogi das Cruzes (UMC), Brazil
| | - David Aciole Barbosa
- Núcleo Integrado de Biotecnologia, Universidade de Mogi das Cruzes (UMC), Brazil
| | - Fabiano B Menegidio
- Núcleo Integrado de Biotecnologia, Universidade de Mogi das Cruzes (UMC), Brazil
| | | | | | - Valquíria C Alencar
- Núcleo Integrado de Biotecnologia, Universidade de Mogi das Cruzes (UMC), Brazil
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC (UFABC), Brazil
| | - Juliana F S Silva
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC (UFABC), Brazil
| | | | - Miguel L Batista
- Núcleo Integrado de Biotecnologia, Universidade de Mogi das Cruzes (UMC), Brazil
- Department of Biochemistry, Boston University School of Medicine, USA
| | - Luiz R Nunes
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC (UFABC), Brazil
| | - Daniela L Jabes
- Núcleo Integrado de Biotecnologia, Universidade de Mogi das Cruzes (UMC), Brazil
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29
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Rahman-Enyart A, Yang W, Yaggie RE, White BA, Welge M, Auvil L, Berry M, Bushell C, Rosen JM, Rudick CN, Schaeffer AJ, Klumpp DJ. Acyloxyacyl hydrolase is a host determinant of gut microbiome-mediated pelvic pain. Am J Physiol Regul Integr Comp Physiol 2021; 321:R396-R412. [PMID: 34318715 PMCID: PMC8530758 DOI: 10.1152/ajpregu.00106.2021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 06/24/2021] [Accepted: 07/16/2021] [Indexed: 12/30/2022]
Abstract
Dysbiosis of gut microbiota is associated with many pathologies, yet host factors modulating microbiota remain unclear. Interstitial cystitis/bladder pain syndrome (IC/BPS) is a debilitating condition of chronic pelvic pain often with comorbid urinary dysfunction and anxiety/depression, and recent studies find fecal dysbiosis in patients with IC/BPS. We identified the locus encoding acyloxyacyl hydrolase, Aoah, as a modulator of pelvic pain severity in a murine IC/BPS model. AOAH-deficient mice spontaneously develop rodent correlates of pelvic pain, increased responses to induced pelvic pain models, voiding dysfunction, and anxious/depressive behaviors. Here, we report that AOAH-deficient mice exhibit dysbiosis of gastrointestinal (GI) microbiota. AOAH-deficient mice exhibit an enlarged cecum, a phenotype long associated with germ-free rodents, and a "leaky gut" phenotype. AOAH-deficient ceca showed altered gene expression consistent with inflammation, Wnt signaling, and urologic disease. 16S sequencing of stool revealed altered microbiota in AOAH-deficient mice, and GC-MS identified altered metabolomes. Cohousing AOAH-deficient mice with wild-type mice resulted in converged microbiota and altered predicted metagenomes. Cohousing also abrogated the pelvic pain phenotype of AOAH-deficient mice, which was corroborated by oral gavage of AOAH-deficient mice with stool slurry of wild-type mice. Converged microbiota also alleviated comorbid anxiety-like behavior in AOAH-deficient mice. Oral gavage of AOAH-deficient mice with anaerobes cultured from IC/BPS stool resulted in exacerbation of pelvic allodynia. Together, these data indicate that AOAH is a host determinant of normal gut microbiota, and dysbiosis associated with AOAH deficiency contributes to pelvic pain. These findings suggest that the gut microbiome is a potential therapeutic target for IC/BPS.
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Affiliation(s)
- Afrida Rahman-Enyart
- Department of Urology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Wenbin Yang
- Division of Thoracic Surgery, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Ryan E Yaggie
- Department of Urology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Bryan A White
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois
- National Center for Supercomputing Applications, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - Michael Welge
- National Center for Supercomputing Applications, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - Loretta Auvil
- National Center for Supercomputing Applications, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - Matthew Berry
- National Center for Supercomputing Applications, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - Colleen Bushell
- National Center for Supercomputing Applications, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - John M Rosen
- Department of Gastroenterology, Children's Mercy, Kansas City, Missouri
- Department of Pediatrics, University of Missouri, Kansas City, Missouri
| | - Charles N Rudick
- Clinical Pharmacology and Toxicology, Indiana University School of Medicine, Bloomington, Indiana
| | - Anthony J Schaeffer
- Department of Urology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - David J Klumpp
- Department of Urology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
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30
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Illescas O, Rodríguez-Sosa M, Gariboldi M. Mediterranean Diet to Prevent the Development of Colon Diseases: A Meta-Analysis of Gut Microbiota Studies. Nutrients 2021; 13:nu13072234. [PMID: 34209683 PMCID: PMC8308215 DOI: 10.3390/nu13072234] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 06/23/2021] [Accepted: 06/25/2021] [Indexed: 02/06/2023] Open
Abstract
Gut microbiota dysbiosis is a common feature in colorectal cancer (CRC) and inflammatory bowel diseases (IBD). Adoption of the Mediterranean diet (MD) has been proposed as a therapeutic approach for the prevention of multiple diseases, and one of its mechanisms of action is the modulation of the microbiota. We aimed to determine whether MD can be used as a preventive measure against cancer and inflammation-related diseases of the gut, based on its capacity to modulate the local microbiota. A joint meta-analysis of publicly available 16S data derived from subjects following MD or other diets and from patients with CRC, IBD, or other gut-related diseases was conducted. We observed that the microbiota associated with MD was enriched in bacteria that promote an anti-inflammatory environment but low in taxa with pro-inflammatory properties capable of altering intestinal barrier functions. We found an opposite trend in patients with intestinal diseases, including cancer. Some of these differences were maintained even when MD was compared to healthy controls without a defined diet. Our findings highlight the unique effects of MD on the gut microbiota and suggest that integrating MD principles into a person’s lifestyle may serve as a preventive method against cancer and other gut-related diseases.
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Affiliation(s)
- Oscar Illescas
- Genetic Epidemiology and Pharmacogenomics Unit, Department of Research, Fondazione IRCCS Istituto Nazionale dei Tumori (INT), 20133 Milan, Italy;
| | - Miriam Rodríguez-Sosa
- Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México (UNAM), Tlalnepantla C.P. 54090, MEX, Mexico;
| | - Manuela Gariboldi
- Genetic Epidemiology and Pharmacogenomics Unit, Department of Research, Fondazione IRCCS Istituto Nazionale dei Tumori (INT), 20133 Milan, Italy;
- Correspondence: ; Tel.: +39-2-23902042
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He Y, Wang Q, Li X, Wang G, Zhao J, Zhang H, Chen W. Lactic acid bacteria alleviate polycystic ovarian syndrome by regulating sex hormone related gut microbiota. Food Funct 2021; 11:5192-5204. [PMID: 32441726 DOI: 10.1039/c9fo02554e] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Polycystic ovarian syndrome (PCOS) is a common endocrine disease across the world. Because gut microbiota play a key role in the pathogenesis of PCOS, probiotics may alleviate PCOS symptoms through the regulation of intestinal flora. The effects of 8 lactic acid bacterial strains on PCOS were investigated. Letrozole was used to produce a PCOS rat model and a 4-week-strain-intervention was performed. Diane-35, as a clinical PCOS treatment medicine, was effective in attenuating rats' reproductive disorders. Lactobacillus plantarum HL2 was protective against ovary pathological changes and restored luteinizing hormone, follicle stimulating hormone and testosterone levels. Bifidobacterium longum HB3 also alleviated ovary abnormalities and decreased testosterone levels. Administration of lactic acid bacteria up-regulated short-chain fatty acid levels. Based on 16S rRNA sequencing, lactic acid bacteria improved letrozole induced gut microbiota dysbiosis with different degrees. Akkermansia, Roseburia, Prevotella, Staphylococcus and Lactobacillus genera were correlated with sex hormone levels. Some of the sex hormone-related gut microbiota were restored by treatment with the strains. These results demonstrated that lactic acid bacteria alleviated PCOS in a rat model by regulating sex hormone related gut microbiota. Modifying gut microbiota by probiotic interventions may thus be a promising therapeutic option for PCOS.
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Affiliation(s)
- Yufeng He
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, PR China. and School of Food Science and Technology, Jiangnan University, Wuxi 214122, PR China
| | - Qianqian Wang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, PR China. and School of Food Science and Technology, Jiangnan University, Wuxi 214122, PR China
| | - Xiu Li
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, PR China. and School of Food Science and Technology, Jiangnan University, Wuxi 214122, PR China
| | - Gang Wang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, PR China. and School of Food Science and Technology, Jiangnan University, Wuxi 214122, PR China and International Joint Research Laboratory for Probiotics, Jiangnan University, Wuxi 214122, PR China and (Yangzhou) Institute of Food Biotechnology, Jiangnan University, Yangzhou 225004, PR China
| | - Jianxin Zhao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, PR China. and School of Food Science and Technology, Jiangnan University, Wuxi 214122, PR China and (Yangzhou) Institute of Food Biotechnology, Jiangnan University, Yangzhou 225004, PR China
| | - Hao Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, PR China. and School of Food Science and Technology, Jiangnan University, Wuxi 214122, PR China and (Yangzhou) Institute of Food Biotechnology, Jiangnan University, Yangzhou 225004, PR China and National Engineering Research Center for Functional Food, Jiangnan University, Wuxi 214122, PR China and Wuxi Translational Medicine Research Center and Jiangsu Translational Medicine Research Institute Wuxi Branch, Wuxi 214122, P. R. China
| | - Wei Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, PR China. and School of Food Science and Technology, Jiangnan University, Wuxi 214122, PR China and National Engineering Research Center for Functional Food, Jiangnan University, Wuxi 214122, PR China and Beijing Innovation Centre of Food Nutrition and Human Health, Beijing Technology and Business University (BTBU), Beijing 100048, PR China
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Aldars-García L, Chaparro M, Gisbert JP. Systematic Review: The Gut Microbiome and Its Potential Clinical Application in Inflammatory Bowel Disease. Microorganisms 2021; 9:microorganisms9050977. [PMID: 33946482 PMCID: PMC8147118 DOI: 10.3390/microorganisms9050977] [Citation(s) in RCA: 74] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 04/22/2021] [Accepted: 04/29/2021] [Indexed: 02/07/2023] Open
Abstract
Inflammatory bowel disease (IBD) is a chronic relapsing-remitting systemic disease of the gastrointestinal tract. It is well established that the gut microbiome has a profound impact on IBD pathogenesis. Our aim was to systematically review the literature on the IBD gut microbiome and its usefulness to provide microbiome-based biomarkers. A systematic search of the online bibliographic database PubMed from inception to August 2020 with screening in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines was conducted. One-hundred and forty-four papers were eligible for inclusion. There was a wide heterogeneity in microbiome analysis methods or experimental design. The IBD intestinal microbiome was generally characterized by reduced species richness and diversity, and lower temporal stability, while changes in the gut microbiome seemed to play a pivotal role in determining the onset of IBD. Multiple studies have identified certain microbial taxa that are enriched or depleted in IBD, including bacteria, fungi, viruses, and archaea. The two main features in this sense are the decrease in beneficial bacteria and the increase in pathogenic bacteria. Significant differences were also present between remission and relapse IBD status. Shifts in gut microbial community composition and abundance have proven to be valuable as diagnostic biomarkers. The gut microbiome plays a major role in IBD, yet studies need to go from casualty to causality. Longitudinal designs including newly diagnosed treatment-naïve patients are needed to provide insights into the role of microbes in the onset of intestinal inflammation. A better understanding of the human gut microbiome could provide innovative targets for diagnosis, prognosis, treatment and even cure of this relevant disease.
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Affiliation(s)
- Laila Aldars-García
- Hospital Universitario de La Princesa, Instituto de Investigación Sanitaria Princesa (IIS-IP), Universidad Autónoma de Madrid, 28006 Madrid, Spain; (L.A.-G.); (M.C.)
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), 28006 Madrid, Spain
| | - María Chaparro
- Hospital Universitario de La Princesa, Instituto de Investigación Sanitaria Princesa (IIS-IP), Universidad Autónoma de Madrid, 28006 Madrid, Spain; (L.A.-G.); (M.C.)
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), 28006 Madrid, Spain
| | - Javier P. Gisbert
- Hospital Universitario de La Princesa, Instituto de Investigación Sanitaria Princesa (IIS-IP), Universidad Autónoma de Madrid, 28006 Madrid, Spain; (L.A.-G.); (M.C.)
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), 28006 Madrid, Spain
- Correspondence: ; Tel.: +34-913-093-911; Fax: +34-915-204-013
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Lin DP, Jin YL, Hu DY, Ying SJ, Jiang Y. Influence of TRAIL Deficiency on Th17 Cells and Colonic Microbiota in Experimental Colitis Mouse Model. Am J Med Sci 2021; 362:188-197. [PMID: 33932348 DOI: 10.1016/j.amjms.2021.04.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Revised: 10/21/2020] [Accepted: 04/21/2021] [Indexed: 11/26/2022]
Abstract
BACKGROUND The abnormalities of tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) are implicated in various autoimmune disorders and tumors. This study investigated the influence of TRAIL deficiency on Th17 cells and colonic microbiota in experimental colitis mouse model. METHODS Mice were randomly divided into 4 groups: wild-type, TRAIL gene knock-out (TRAIL-/-), wild-type colitis and TRAIL-/- colitis groups. Colitis was induced by oral administration of 3.5% dextran sulfate sodium (DSS) for 7 consecutive days. Mice were given scores for disease severity both clinically and histopathologically. Th17 cells in peripheral blood and mesenteric lymph nodes (MLNs) were assessed using flow cytometry. The expression levels of Th17 cell markers IL-17A and ROR-γt were evaluated by quantitative real-time polymerase chain reaction. The colonic samples were also analyzed for microbiota profile by 16s-rDNA gene sequencing on variable V4 region. RESULTS Compared with wild-type counterparts, TRAIL-/- mice developed more severe colitis after DSS treatment. Colitis TRAIL-/- mice had increased proportion of Th17 cells and elevated mRNA expression levels of IL-17A and ROR-γt in peripheral blood and MLNs compared with colitis wild-type mice. In contrast to colitis wild-type mice, the composition of colonic microbiota was shifted in colitis TRAIL-/- mice, and was characterized by increased alpha diversity, increased TM7, deferribacteres and tenericutes, and decreased proteobacteria at the phylum level. CONCLUSIONS These findings suggested that TRAIL deficiency not only aggravated DSS-induced colitis, but also led to enhanced Th17 cell response and altered colonic microbiota composition.
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Affiliation(s)
- Dao-Po Lin
- Department of Gastroenterology, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Ying-Li Jin
- Department of Gastroenterology, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Ding-Yuan Hu
- Department of Gastroenterology, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Shi-Jie Ying
- Department of Gastroenterology, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Yi Jiang
- Department of Gastroenterology, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, China.
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34
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McLean JS, Bor B, Kerns KA, Liu Q, To TT, Solden L, Hendrickson EL, Wrighton K, Shi W, He X. Acquisition and Adaptation of Ultra-small Parasitic Reduced Genome Bacteria to Mammalian Hosts. Cell Rep 2021; 32:107939. [PMID: 32698001 PMCID: PMC7427843 DOI: 10.1016/j.celrep.2020.107939] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 06/20/2020] [Accepted: 06/30/2020] [Indexed: 12/31/2022] Open
Abstract
The first cultivated representative of the enigmatic phylum Saccharibacteria (formerly TM7) was isolated from humans and revealed an ultra-small cell size (200-300 nm), a reduced genome with limited biosynthetic capabilities, and a unique parasitic lifestyle. TM7x was the only cultivated member of the candidate phyla radiation (CPR), estimated to encompass 26% of the domain Bacteria. Here we report on divergent genomes from major lineages across the Saccharibacteria phylum in humans and mammals, as well as from ancient dental calculus. These lineages are present at high prevalence within hosts. Direct imaging reveals that all groups are ultra-small in size, likely feeding off commensal bacteria. Analyses suggest that multiple acquisition events in the past led to the current wide diversity, with convergent evolution of key functions allowing Saccharibacteria from the environment to adapt to mammals. Ultra-small, parasitic CPR bacteria represent a relatively unexplored paradigm of prokaryotic interactions within mammalian microbiomes.
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Affiliation(s)
- Jeffrey S McLean
- Department of Periodontics, University of Washington, Seattle, WA 98195, USA; Department of Microbiology, University of Washington, Seattle, WA 98195, USA.
| | - Batbileg Bor
- Department of Microbiology, The Forsyth Institute, Cambridge, MA 02142, USA; Department of Oral Medicine, Infection and Immunity, Harvard School of Dental Medicine, Boston, MA 02115, USA
| | - Kristopher A Kerns
- Department of Periodontics, University of Washington, Seattle, WA 98195, USA
| | - Quanhui Liu
- Department of Periodontics, University of Washington, Seattle, WA 98195, USA
| | - Thao T To
- Department of Periodontics, University of Washington, Seattle, WA 98195, USA
| | - Lindsey Solden
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA
| | - Erik L Hendrickson
- Department of Periodontics, University of Washington, Seattle, WA 98195, USA
| | - Kelly Wrighton
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA
| | - Wenyuan Shi
- Department of Microbiology, The Forsyth Institute, Cambridge, MA 02142, USA
| | - Xuesong He
- Department of Microbiology, The Forsyth Institute, Cambridge, MA 02142, USA; Department of Oral Medicine, Infection and Immunity, Harvard School of Dental Medicine, Boston, MA 02115, USA
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35
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Cui J, Fu Y, Yi Z, Dong C, Liu H. The beneficial effects of ultraviolet light supplementation on bone density are associated with the intestinal flora in rats. Appl Microbiol Biotechnol 2021; 105:3705-3715. [PMID: 33893837 DOI: 10.1007/s00253-021-11282-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 03/22/2021] [Accepted: 04/07/2021] [Indexed: 01/14/2023]
Abstract
The general public spends one-third of its time under artificial lighting, which lacks bands beneficial to human health, and long-term exposure will have a negative impact on bone health. Here, we report the effects of long-term, low-dose ultraviolet (UV) supplementation to white light-emitting diode (LED) light exposure on intestinal microorganisms and bone metabolism, as well as the correlations between the two. Normal and ovariectomized rats were irradiated with LED white light with or without supplementation with UV. The effects of UV supplementation on the intestinal flora and the relationship between the intestinal flora and bone were investigated by measuring the intestinal flora, bone metabolism markers, and bone histomorphology. UV supplementation affected the bone density and bone mass by changing the relative content of Firmicutes, Saccharibacteria, and Proteobacteria; however, the intestinal flora were not the only factors affecting bone. Ultraviolet supplementation changed the composition and function of the gut flora in the bone loss model. By increasing the synthesis of short-chain fatty acids and affecting immunomodulatory, intestinal flora directly or indirectly regulate the activity of osteoclasts and thus mediate UV-mediated improvements in bone metabolism. Our work shows that UV supplementation affects bone density by influencing the intestinal flora, introducing a novel strategy to develop healthier artificial light sources and prevent bone loss. KEY POINTS: • We measured the bone metabolism markers and bone histomorphometry of rats. • The diversity, composition, and function of intestinal flora were analyzed. • The relationship between gut microbiota and host bone physiology was analyzed.
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Affiliation(s)
- Jingjing Cui
- Key Laboratory for Biomechanics and Mechanobiology of the Ministry of Education, Beijing Advanced Innovation Centre for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing, 100191, China.,International Joint Research Center of Aerospace Biotechnology & Medical Engineering, Beihang University, Beijing, 100191, China.,State Key Laboratory of Virtual Reality Technology and Systems, School of Computer Science and Engineering, Beihang University, No.37 Xueyuan Road, Beijing, 100083, China
| | - Yuming Fu
- Key Laboratory for Biomechanics and Mechanobiology of the Ministry of Education, Beijing Advanced Innovation Centre for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing, 100191, China. .,International Joint Research Center of Aerospace Biotechnology & Medical Engineering, Beihang University, Beijing, 100191, China. .,State Key Laboratory of Virtual Reality Technology and Systems, School of Computer Science and Engineering, Beihang University, No.37 Xueyuan Road, Beijing, 100083, China.
| | - Zhihao Yi
- Key Laboratory for Biomechanics and Mechanobiology of the Ministry of Education, Beijing Advanced Innovation Centre for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing, 100191, China.,International Joint Research Center of Aerospace Biotechnology & Medical Engineering, Beihang University, Beijing, 100191, China.,State Key Laboratory of Virtual Reality Technology and Systems, School of Computer Science and Engineering, Beihang University, No.37 Xueyuan Road, Beijing, 100083, China
| | - Chen Dong
- School of Sport Social Science, Shandong Sport University, Jinan, 250102, China
| | - Hong Liu
- Key Laboratory for Biomechanics and Mechanobiology of the Ministry of Education, Beijing Advanced Innovation Centre for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing, 100191, China.,International Joint Research Center of Aerospace Biotechnology & Medical Engineering, Beihang University, Beijing, 100191, China.,State Key Laboratory of Virtual Reality Technology and Systems, School of Computer Science and Engineering, Beihang University, No.37 Xueyuan Road, Beijing, 100083, China
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Laswi I, Shafiq A, Al-Ali D, Burney Z, Pillai K, Salameh M, Mhaimeed N, Zakaria D, Chaari A, Yousri NA, Bendriss G. A Comparative Pilot Study of Bacterial and Fungal Dysbiosis in Neurodevelopmental Disorders and Gastrointestinal Disorders: Commonalities, Specificities and Correlations with Lifestyle. Microorganisms 2021; 9:741. [PMID: 33918112 PMCID: PMC8065742 DOI: 10.3390/microorganisms9040741] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 03/24/2021] [Accepted: 03/25/2021] [Indexed: 01/15/2023] Open
Abstract
Gastrointestinal disorders (GIDs) are a common comorbidity in patients with neurodevelopmental disorders (NDDs), while anxiety-like behaviors are common among patients with gastrointestinal diseases. It is still unclear as to which microbes differentiate these two groups. This pilot study aims at proposing an answer by exploring both the bacteriome and the mycobiome in a cohort of 55 volunteers with NDD, GID or controls, while accounting for additional variables that are not commonly included such as probiotic intake and diet. Recruited participants answered a questionnaire and provided a stool sample using the Fisherbrand collection kit. Bacterial and fungal DNA was extracted using the Qiagen Stool minikit. Sequencing (16sRNA and ITS) and phylogenetic analyses were performed using the PE300 Illumina Miseq v3 sequencing. Statistical analysis was performed using the R package. Results showed a significant decrease in bacterial alpha diversity in both NDD and GID, but an increased fungal alpha diversity in NDD. Data pointed at a significant bacterial dysbiosis between the three groups, but the mycobiome dysbiosis is more pronounced in NDD than in GID. Fungi seem to be more affected by probiotics, diet and antibiotic exposure and are proposed to be the main key player in differentiation between NDD and GID dybiosis.
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Affiliation(s)
- Ibrahim Laswi
- Premedical Education Department, Weill Cornell Medicine Qatar, Doha 24144, Qatar; (I.L.); (A.S.); (D.A.-A.); (Z.B.); (K.P.); (M.S.); (N.M.); (D.Z.); (A.C.)
| | - Ameena Shafiq
- Premedical Education Department, Weill Cornell Medicine Qatar, Doha 24144, Qatar; (I.L.); (A.S.); (D.A.-A.); (Z.B.); (K.P.); (M.S.); (N.M.); (D.Z.); (A.C.)
| | - Dana Al-Ali
- Premedical Education Department, Weill Cornell Medicine Qatar, Doha 24144, Qatar; (I.L.); (A.S.); (D.A.-A.); (Z.B.); (K.P.); (M.S.); (N.M.); (D.Z.); (A.C.)
| | - Zain Burney
- Premedical Education Department, Weill Cornell Medicine Qatar, Doha 24144, Qatar; (I.L.); (A.S.); (D.A.-A.); (Z.B.); (K.P.); (M.S.); (N.M.); (D.Z.); (A.C.)
| | - Krishnadev Pillai
- Premedical Education Department, Weill Cornell Medicine Qatar, Doha 24144, Qatar; (I.L.); (A.S.); (D.A.-A.); (Z.B.); (K.P.); (M.S.); (N.M.); (D.Z.); (A.C.)
| | - Mohammad Salameh
- Premedical Education Department, Weill Cornell Medicine Qatar, Doha 24144, Qatar; (I.L.); (A.S.); (D.A.-A.); (Z.B.); (K.P.); (M.S.); (N.M.); (D.Z.); (A.C.)
| | - Nada Mhaimeed
- Premedical Education Department, Weill Cornell Medicine Qatar, Doha 24144, Qatar; (I.L.); (A.S.); (D.A.-A.); (Z.B.); (K.P.); (M.S.); (N.M.); (D.Z.); (A.C.)
| | - Dalia Zakaria
- Premedical Education Department, Weill Cornell Medicine Qatar, Doha 24144, Qatar; (I.L.); (A.S.); (D.A.-A.); (Z.B.); (K.P.); (M.S.); (N.M.); (D.Z.); (A.C.)
| | - Ali Chaari
- Premedical Education Department, Weill Cornell Medicine Qatar, Doha 24144, Qatar; (I.L.); (A.S.); (D.A.-A.); (Z.B.); (K.P.); (M.S.); (N.M.); (D.Z.); (A.C.)
| | - Noha A. Yousri
- Research Department, Weill Cornell Medicine Qatar, Doha 24144, Qatar;
- Computers and System Engineering, Alexandria University, Alexandria 21526, Egypt
| | - Ghizlane Bendriss
- Premedical Education Department, Weill Cornell Medicine Qatar, Doha 24144, Qatar; (I.L.); (A.S.); (D.A.-A.); (Z.B.); (K.P.); (M.S.); (N.M.); (D.Z.); (A.C.)
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Transverse aortic constriction induces gut barrier alterations, microbiota remodeling and systemic inflammation. Sci Rep 2021; 11:7404. [PMID: 33795775 PMCID: PMC8016915 DOI: 10.1038/s41598-021-86651-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 03/15/2021] [Indexed: 12/27/2022] Open
Abstract
Accumulating evidence suggests that modifications of gut function and microbiota composition might play a pivotal role in the pathophysiology of several cardiovascular diseases, including heart failure (HF). In this study we systematically analysed gut microbiota composition, intestinal barrier integrity, intestinal and serum cytokines and serum endotoxin levels in C57BL/6 mice undergoing pressure overload by transverse aortic constriction (TAC) for 1 and 4 weeks. Compared to sham-operated animals, TAC induced prompt and strong weakening of intestinal barrier integrity, long-lasting decrease of colon anti-inflammatory cytokine levels, significant increases of serum levels of bacterial lipopolysaccharide and proinflammatory cytokines. TAC also exerted effects on microbiota composition, inducing significant differences in bacterial genera inside Actinobacteria, Firmicutes, Proteobacteria and TM7 phyla as shown by 16S rDNA sequencing of fecal samples from TAC or sham mice. These results suggest that gut modifications represent an important element to be considered in the development and progression of cardiac dysfunction in response to TAC and support this animal model as a valuable tool to establish the role and mechanisms of gut-heart crosstalk in HF. Evidence arising in this field might identify new treatment options targeting gut integrity and microbiota components to face adverse cardiac events.
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Hereditary hemochromatosis promotes colitis and colon cancer and causes bacterial dysbiosis in mice. Biochem J 2021; 477:3867-3883. [PMID: 32955078 PMCID: PMC7557149 DOI: 10.1042/bcj20200392] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 09/17/2020] [Accepted: 09/21/2020] [Indexed: 12/24/2022]
Abstract
Hereditary hemochromatosis (HH), an iron-overload disease, is a prevalent genetic disorder. As excess iron causes a multitude of metabolic disturbances, we postulated that iron overload in HH disrupts colonic homeostasis and colon–microbiome interaction and exacerbates the development and progression of colonic inflammation and colon cancer. To test this hypothesis, we examined the progression and severity of colitis and colon cancer in a mouse model of HH (Hfe−/−), and evaluated the potential contributing factors. We found that experimentally induced colitis and colon cancer progressed more robustly in Hfe−/− mice than in wild-type mice. The underlying causes were multifactorial. Hfe−/− colons were leakier with lower proliferation capacity of crypt cells, which impaired wound healing and amplified inflammation-driven tissue injury. The host/microflora axis was also disrupted. Sequencing of fecal 16S RNA revealed profound changes in the colonic microbiome in Hfe−/− mice in favor of the pathogenic bacteria belonging to phyla Proteobacteria and TM7. There was an increased number of bacteria adhered onto the mucosal surface of the colonic epithelium in Hfe−/− mice than in wild-type mice. Furthermore, the expression of innate antimicrobial peptides, the first-line of defense against bacteria, was lower in Hfe−/− mouse colon than in wild-type mouse colon; the release of pro-inflammatory cytokines upon inflammatory stimuli was also greater in Hfe−/− mouse colon than in wild-type mouse colon. These data provide evidence that excess iron accumulation in colonic tissue as happens in HH promotes colitis and colon cancer, accompanied with bacterial dysbiosis and loss of function of the intestinal/colonic barrier.
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Lu Y, Yang J, Dong C, Fu Y, Liu H. Gut microbiome-mediated changes in bone metabolism upon infrared light exposure in rats. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2021; 217:112156. [PMID: 33647735 DOI: 10.1016/j.jphotobiol.2021.112156] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 12/25/2020] [Accepted: 02/15/2021] [Indexed: 12/14/2022]
Abstract
Adequate sunlight exposure helps reduce bone loss and is important to bone health. Currently, about 90% of the world population spends a major portion of daily life under artificial lighting. Unlike sunlight, LED white light, the main source of artificial lighting, has no infrared radiation, which is known to be beneficial to human health. In artificial lighting environments, infrared supplementation may be used to simulate the effects of sunlight on bone metabolism. Here, we supplemented white LED exposure with infrared light in normal and ovariectomized rats for three consecutive months and examined bone turnover, bone mass, and bone density. We also analyzed the structure and function of gut microbiota in the rats. Infrared supplementation significantly reduced the abundance of Saccharibacteria and increased the abundance of Clostridiaceae 1 and Erysipelotrichaceae bacteria. Our results indicate that changes in the gut microbiome correlate well with bone mass and bone metabolism. Our work demonstrates that infrared supplementation can have a positive effect on rat bone metabolism by affecting gut microbiota. Our findings will be important considerations in the future design of healthy lighting environments that prevent or possibly ameliorate osteoporosis.
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Affiliation(s)
- Yueying Lu
- Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing 100191, China; International Joint Research Center of Aerospace Biotechnology & Medical Engineering, Beihang University, Beijing 100191, China; State Key Laboratory of Virtual Reality Technology and Systems, School of Computer Science and Engineering, Beihang University, Beijing 100083, China.
| | - Jianlou Yang
- Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing 100191, China; International Joint Research Center of Aerospace Biotechnology & Medical Engineering, Beihang University, Beijing 100191, China; State Key Laboratory of Virtual Reality Technology and Systems, School of Computer Science and Engineering, Beihang University, Beijing 100083, China
| | - Chen Dong
- Laboratory of Sport Nutrition and Intelligent Cooking, Shandong Sport University, Jinan 250102,China.
| | - Yuming Fu
- Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing 100191, China; International Joint Research Center of Aerospace Biotechnology & Medical Engineering, Beihang University, Beijing 100191, China; State Key Laboratory of Virtual Reality Technology and Systems, School of Computer Science and Engineering, Beihang University, Beijing 100083, China.
| | - Hong Liu
- Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing 100191, China; International Joint Research Center of Aerospace Biotechnology & Medical Engineering, Beihang University, Beijing 100191, China; State Key Laboratory of Virtual Reality Technology and Systems, School of Computer Science and Engineering, Beihang University, Beijing 100083, China.
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Yu Y, Wang Z, Wang R, Jin J, Zhu YZ. Short-Term Oral Administration of Mesoporous Silica Nanoparticles Potentially Induced Colon Inflammation in Rats Through Alteration of Gut Microbiota. Int J Nanomedicine 2021; 16:881-893. [PMID: 33574668 PMCID: PMC7872941 DOI: 10.2147/ijn.s295575] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 01/21/2021] [Indexed: 11/23/2022] Open
Abstract
PURPOSE Mesoporous silica (MSNs) have attracted considerable attention for its application in the field of drug delivery and biomedicine due to its high surface area, large pore volume, and low toxicity. Recently, numerous studies revealed that gut microbiota is of critical relevance to host health. However, the toxicological studies of MSNs were mainly based on the degradation, biodistribution, and excretion in mammalian after oral administration for now. Here in this study, we explored the impacts of oral administration of three kinds of MSNs on gut microbiota in rats to assess its potential toxicity. METHODS Forty rats were divided into four groups: control group; Mobil Composition of Matter No. 41 type mesoporous silica (MCM-41) group; Santa Barbara Amorphous-15 type mesoporous silica (SBA-15) group, and biodegradable dendritic center-radial mesoporous silica nanoparticle (DMSN) group. Fecal samples were collected 3 days and 7 days after the intake of MSNs and analyzed with high throughput sequencing. Gastric tissues in rats were obtained after dissection for the histological study. RESULTS Three different MSNs (MCM-41, SBA-15, and DMSN) were successfully prepared in this study. The pore size of three MSNs was calculated similarly as (3.54 ± 0.15) nm, (3.48 ± 0.21) nm, and (3.45 ± 0.17) nm according to the BET & BJH model, respectively, while the particle size of MCM-41, SBA-15 and DMSN was around 209.2 nm, 1349.56 nm, and 244.4 nm, respectively. In the gene analysis of 16S rRNA, no significant changes in the diversity and richness were found between groups, while Verrucomicrobia decreased and Candidatus Saccharibacteria increased in MCM-41 treated groups. Meanwhile, no inflammatory and erosion symptoms were observed in the morphological analysis of the colons, except the MCM-41 treated group. CONCLUSION Three different MSNs, MCM-41, SBA-15, and DMSN were successfully prepared, and this study firstly suggested the impact of MSNs on the gut microbiota, and further revealing the potential pro-inflammatory effects of oral administration of MCM-41 was possibly through the changing of gut microbiota.
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Affiliation(s)
- Yue Yu
- State Key Laboratory of Quality Research in Chinese Medicine & School of Pharmacy, Macau University of Science and Technology, Taipa, Macau SAR, People’s Republic of China
| | - Zhou Wang
- State Key Laboratory of Quality Research in Chinese Medicine & School of Pharmacy, Macau University of Science and Technology, Taipa, Macau SAR, People’s Republic of China
| | - Ran Wang
- State Key Laboratory of Quality Research in Chinese Medicine & School of Pharmacy, Macau University of Science and Technology, Taipa, Macau SAR, People’s Republic of China
| | - Jing Jin
- Institute of Material Medica, Chinese Academy of Medical Sciences, Beijing, People’s Republic of China
| | - Yi Zhun Zhu
- State Key Laboratory of Quality Research in Chinese Medicine & School of Pharmacy, Macau University of Science and Technology, Taipa, Macau SAR, People’s Republic of China
- Shanghai Key Laboratory of Bioactive Small Molecules & School of Pharmacy, Fudan University, Shanghai, People’s Republic of China
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Effects of Essential Oils-Based Supplement and Salmonella Infection on Gene Expression, Blood Parameters, Cecal Microbiome, and Egg Production in Laying Hens. Animals (Basel) 2021; 11:ani11020360. [PMID: 33535430 PMCID: PMC7912222 DOI: 10.3390/ani11020360] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Revised: 01/26/2021] [Accepted: 01/28/2021] [Indexed: 11/17/2022] Open
Abstract
One of the main roles in poultry resistance to infections caused by Salmonella is attributed to host immunity and intestinal microbiota. We conducted an experiment that involved challenging Lohmann White laying hens with Salmonella Enteritidis (SE), feeding them a diet supplemented with an EOs-based phytobiotic Intebio®. At 1 and 7 days post-inoculation, the expression profiles of eight genes related to immunity, transport of nutrients in the intestine, and metabolism were examined. Cecal microbiome composition and blood biochemical/immunological indices were also explored and egg production traits recorded. As a result, the SE challenge of laying hens and Intebio® administration had either a suppressive or activating effect on the expression level of the studied genes (e.g., IL6 and BPIFB3), the latter echoing mammalian/human tissue-specific expression. There were also effects of the pathogen challenge and phytobiotic intake on the cecal microbiome profiles and blood biochemical/immunological parameters, including those reflecting the activity of the birds' immune systems (e.g., serum bactericidal activity, β-lysine content, and immunoglobulin levels). Significant differences between control and experimental subgroups in egg performance traits (i.e., egg weight/number/mass) were also found. The phytobiotic administration suggested a positive effect on the welfare and productivity of poultry.
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Genome-resolved metagenomics reveals site-specific diversity of episymbiotic CPR bacteria and DPANN archaea in groundwater ecosystems. Nat Microbiol 2021; 6:354-365. [PMID: 33495623 PMCID: PMC7906910 DOI: 10.1038/s41564-020-00840-5] [Citation(s) in RCA: 79] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Accepted: 11/20/2020] [Indexed: 11/16/2022]
Abstract
Candidate phyla radiation (CPR) bacteria and DPANN archaea are unisolated, small-celled symbionts that are often detected in groundwater. The effects of groundwater geochemistry on the abundance, distribution, taxonomic diversity and host association of CPR bacteria and DPANN archaea has not been studied. Here, we performed genome-resolved metagenomic analysis of one agricultural and seven pristine groundwater microbial communities and recovered 746 CPR and DPANN genomes in total. The pristine sites, which serve as local sources of drinking water, contained up to 31% CPR bacteria and 4% DPANN archaea. We observed little species-level overlap of metagenome-assembled genomes (MAGs) across the groundwater sites, indicating that CPR and DPANN communities may be differentiated according to physicochemical conditions and host populations. Cryogenic transmission electron microscopy imaging and genomic analyses enabled us to identify CPR and DPANN lineages that reproducibly attach to host cells and showed that the growth of CPR bacteria seems to be stimulated by attachment to host-cell surfaces. Our analysis reveals site-specific diversity of CPR bacteria and DPANN archaea that coexist with diverse hosts in groundwater aquifers. Given that CPR and DPANN organisms have been identified in human microbiomes and their presence is correlated with diseases such as periodontitis, our findings are relevant to considerations of drinking water quality and human health. Metagenomics and electron microscopy are combined to analyse the diversity of episymbiotic CPR bacteria and DPANN archaea in eight groundwater communities.
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Pistollato F, Forbes-Hernandez TY, Iglesias RC, Ruiz R, Elexpuru Zabaleta M, Dominguez I, Cianciosi D, Quiles JL, Giampieri F, Battino M. Effects of caloric restriction on immunosurveillance, microbiota and cancer cell phenotype: Possible implications for cancer treatment. Semin Cancer Biol 2020; 73:45-57. [PMID: 33271317 DOI: 10.1016/j.semcancer.2020.11.017] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 11/24/2020] [Accepted: 11/27/2020] [Indexed: 12/12/2022]
Abstract
Fasting, caloric restriction and foods or compounds mimicking the biological effects of caloric restriction, known as caloric restriction mimetics, have been associated with a lower risk of age-related diseases, including cardiovascular diseases, cancer and cognitive decline, and a longer lifespan. Reduced calorie intake has been shown to stimulate cancer immunosurveillance, reducing the migration of immunosuppressive regulatory T cells towards the tumor bulk. Autophagy stimulation via reduction of lysine acetylation, increased sensitivity to chemo- and immunotherapy, along with a reduction of insulin-like growth factor 1 and reactive oxygen species have been described as some of the major effects triggered by caloric restriction. Fasting and caloric restriction have also been shown to beneficially influence gut microbiota composition, modify host metabolism, reduce total cholesterol and triglyceride levels, lower diastolic blood pressure and elevate morning cortisol level, with beneficial modulatory effects on cardiopulmonary fitness, body fat and weight, fatigue and weakness, and general quality of life. Moreover, caloric restriction may reduce the carcinogenic and metastatic potential of cancer stem cells, which are generally considered responsible of tumor formation and relapse. Here, we reviewed in vitro and in vivo studies describing the effects of fasting, caloric restriction and some caloric restriction mimetics on immunosurveillance, gut microbiota, metabolism, and cancer stem cell growth, highlighting the molecular and cellular mechanisms underlying these effects. Additionally, studies on caloric restriction interventions in cancer patients or cancer risk subjects are discussed. Considering the promising effects associated with caloric restriction and caloric restriction mimetics, we think that controlled-randomized large clinical trials are warranted to evaluate the inclusion of these non-pharmacological approaches in clinical practice.
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Affiliation(s)
- Francesca Pistollato
- Centre for Nutrition and Health, Universidad Europea del Atlántico (UEA), Santander, Spain
| | - Tamara Yuliett Forbes-Hernandez
- Nutrition and Food Science Group, Department of Analytical and Food Chemistry, CITACA, CACTI, University of Vigo, Vigo, Spain
| | | | - Roberto Ruiz
- Centre for Nutrition and Health, Universidad Europea del Atlántico (UEA), Santander, Spain
| | | | - Irma Dominguez
- Universidad Internacional Iberoamericana (UNINI), Camphece, Mexico; Universidade Internacional do Cuanza, Cuito, Angola
| | - Danila Cianciosi
- Dipartimento di Scienze Cliniche Specialistiche ed Odontostomatologiche, Sez. Biochimica, Università Politecnica delle Marche, Ancona, Italy
| | - Josè L Quiles
- Department of Physiology, Institute of Nutrition and Food Technology "Jose Mataix", Biomedical Research Center, University of Granada, Granada, 18000, Spain
| | - Francesca Giampieri
- Dipartimento di Scienze Cliniche Specialistiche ed Odontostomatologiche, Sez. Biochimica, Università Politecnica delle Marche, Ancona, Italy; Department of Biochemistry, Faculty of Sciences, King Abdulaziz University, Jeddah, Saudi Arabia; College of Food Science and Technology, Northwest University, Xi'an, 710069, China.
| | - Maurizio Battino
- Dipartimento di Scienze Cliniche Specialistiche ed Odontostomatologiche, Sez. Biochimica, Università Politecnica delle Marche, Ancona, Italy; International Research Center for Food Nutrition and Safety, Jiangsu University, Zhenjiang, 212013, China.
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State of the Art in the Culture of the Human Microbiota: New Interests and Strategies. Clin Microbiol Rev 2020; 34:34/1/e00129-19. [PMID: 33115723 DOI: 10.1128/cmr.00129-19] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The last 5 years have seen a turning point in the study of the gut microbiota with a rebirth of culture-dependent approaches to study the gut microbiota. High-throughput methods have been developed to study bacterial diversity with culture conditions aimed at mimicking the gut environment by using rich media such as YCFA (yeast extract, casein hydrolysate, fatty acids) and Gifu anaerobic medium in an anaerobic workstation, as well as media enriched with rumen and blood and coculture, to mimic the symbiosis of the gut microbiota. Other culture conditions target phenotypic and metabolic features of bacterial species to facilitate their isolation. Preexisting technologies such as next-generation sequencing and flow cytometry have also been utilized to develop innovative methods to isolate previously uncultured bacteria or explore viability in samples of interest. These techniques have been applied to isolate CPR (Candidate Phyla Radiation) among other, more classic approaches. Methanogenic archaeal and fungal cultures present different challenges than bacterial cultures. Efforts to improve the available systems to grow archaea have been successful through coculture systems. For fungi that are more easily isolated from the human microbiota, the challenge resides in the identification of the isolates, which has been approached by applying matrix-assisted laser desorption ionization-time of flight mass spectrometry technology to fungi. Bacteriotherapy represents a nonnegligible avenue in the future of medicine to correct dysbiosis and improve health or response to therapy. Although great strides have been achieved in the last 5 years, efforts in bacterial culture need to be sustained to continue deciphering the dark matter of metagenomics, particularly CPR, and extend these methods to archaea and fungi.
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Xu F, Fu Y, Sun TY, Jiang Z, Miao Z, Shuai M, Gou W, Ling CW, Yang J, Wang J, Chen YM, Zheng JS. The interplay between host genetics and the gut microbiome reveals common and distinct microbiome features for complex human diseases. MICROBIOME 2020; 8:145. [PMID: 33032658 PMCID: PMC7545574 DOI: 10.1186/s40168-020-00923-9] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 09/13/2020] [Indexed: 05/11/2023]
Abstract
BACKGROUND Interest in the interplay between host genetics and the gut microbiome in complex human diseases is increasing, with prior evidence mainly being derived from animal models. In addition, the shared and distinct microbiome features among complex human diseases remain largely unclear. RESULTS This analysis was based on a Chinese population with 1475 participants. We estimated the SNP-based heritability, which suggested that Desulfovibrionaceae and Odoribacter had significant heritability estimates (0.456 and 0.476, respectively). We performed a microbiome genome-wide association study to identify host genetic variants associated with the gut microbiome. We then conducted bidirectional Mendelian randomization analyses to examine the potential causal associations between the gut microbiome and complex human diseases. We found that Saccharibacteria could potentially decrease the concentration of serum creatinine and increase the estimated glomerular filtration rate. On the other hand, atrial fibrillation, chronic kidney disease and prostate cancer, as predicted by host genetics, had potential causal effects on the abundance of some specific gut microbiota. For example, atrial fibrillation increased the abundance of Burkholderiales and Alcaligenaceae and decreased the abundance of Lachnobacterium, Bacteroides coprophilus, Barnesiellaceae, an undefined genus in the family Veillonellaceae and Mitsuokella. Further disease-microbiome feature analysis suggested that systemic lupus erythematosus and chronic myeloid leukaemia shared common gut microbiome features. CONCLUSIONS These results suggest that different complex human diseases share common and distinct gut microbiome features, which may help reshape our understanding of disease aetiology in humans. Video Abstract.
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Affiliation(s)
- Fengzhe Xu
- Zhejiang Provincial Laboratory of Life Sciences and Biomedicine, Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China
| | - Yuanqing Fu
- Zhejiang Provincial Laboratory of Life Sciences and Biomedicine, Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, China
| | - Ting-Yu Sun
- Guangdong Provincial Key Laboratory of Food, Nutrition and Health, Department of Epidemiology, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Zengliang Jiang
- Zhejiang Provincial Laboratory of Life Sciences and Biomedicine, Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, China
| | - Zelei Miao
- Zhejiang Provincial Laboratory of Life Sciences and Biomedicine, Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China
| | - Menglei Shuai
- Zhejiang Provincial Laboratory of Life Sciences and Biomedicine, Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China
| | - Wanglong Gou
- Zhejiang Provincial Laboratory of Life Sciences and Biomedicine, Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China
| | - Chu-Wen Ling
- Guangdong Provincial Key Laboratory of Food, Nutrition and Health, Department of Epidemiology, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Jian Yang
- Institute for Molecular Bioscience, The University of Queensland, QLD, Brisbane, Australia
- Institute for Advanced Research, Wenzhou Medical University, Wenzhou, 325027, Zhejiang, China
| | - Jun Wang
- CAS Key Laboratory for Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.
| | - Yu-Ming Chen
- Guangdong Provincial Key Laboratory of Food, Nutrition and Health, Department of Epidemiology, School of Public Health, Sun Yat-sen University, Guangzhou, China.
| | - Ju-Sheng Zheng
- Zhejiang Provincial Laboratory of Life Sciences and Biomedicine, Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China.
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, China.
- MRC Epidemiology Unit, University of Cambridge, Cambridge, UK.
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Qi Y, Zang SQ, Wei J, Yu HC, Yang Z, Wu HM, Kang Y, Tao H, Yang MF, Jin L, Zen K, Wang FY. High-throughput sequencing provides insights into oral microbiota dysbiosis in association with inflammatory bowel disease. Genomics 2020; 113:664-676. [PMID: 33010388 DOI: 10.1016/j.ygeno.2020.09.063] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 09/16/2020] [Accepted: 09/29/2020] [Indexed: 12/12/2022]
Abstract
Although the prevalence of inflammatory bowel disease (IBD) has been increasing worldwide, the etiology remains elusive. Investigating oral microbiota dysbiosis is essential to understanding IBD pathogenesis. Our study evaluated variations in salivary microbiota and identified potential associations with IBD. The saliva microbiota of 22 IBD patients and 8 healthy controls (HCs) was determined using 16S ribosomal RNA (rRNA) gene sequencing and analyzed using QIIME2. A distinct saliva microbiota dysbiosis in IBD, characterized by alterations in microbiota biodiversity and composition, was identified. Saccharibacteria (TM7), Absconditabacteria (SR1), Leptotrichia, Prevotella, Bulleidia, and Atopobium, some of which are oral biofilm-forming bacteria, were significantly increased. Moreover, levels of inflammatory cytokines associated with IBD were elevated and positively correlated with TM7 and SR1. Functional variations include down-regulation of genetic information processing, while up-regulation of carbohydrate metabolism and protein processing in the endoplasmic reticulum in IBD. Our data implicate salivary microbiota dysbiosis involving in IBD pathogenesis.
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Affiliation(s)
- Ying Qi
- Department of Gastroenterology and Hepatology, Jinling Hospital, Medical School of Nanjing University, Nanjing, Jiangsu, China
| | - Sheng-Qi Zang
- Department of Stomatology, Jinling Hospital, Nanjing, Jiangsu, China
| | - Juan Wei
- Department of Gastroenterology and Hepatology, Jinling Hospital, Clinical Medical College of Nanjing Medical University, Nanjing, China
| | - Hong-Chuan Yu
- Department of Stomatology, Jinling Hospital, Nanjing, Jiangsu, China
| | - Zhao Yang
- Department of Gastroenterology and Hepatology, Jinling Hospital, Medical School of Nanjing University, Nanjing, Jiangsu, China
| | - Hui-Min Wu
- Department of Gastroenterology and Hepatology, Jinling Hospital, Medical School of Nanjing University, Nanjing, Jiangsu, China
| | - Ying Kang
- Department of Gastroenterology and Hepatology, Jinling Hospital, Medical School of Nanjing University, Nanjing, Jiangsu, China
| | - Hui Tao
- Department of Gastroenterology and Hepatology, Jinling Hospital, Medical School of Nanjing University, Nanjing, Jiangsu, China
| | - Miao-Fang Yang
- Department of Gastroenterology and Hepatology, Jinling Hospital, Medical School of Nanjing University, Nanjing, Jiangsu, China
| | - Lei Jin
- Department of Stomatology, Jinling Hospital, Nanjing, Jiangsu, China
| | - Ke Zen
- School of life sciences, Nanjing University, Nanjing, Jiangsu, China
| | - Fang-Yu Wang
- Department of Gastroenterology and Hepatology, Jinling Hospital, Medical School of Nanjing University, Nanjing, Jiangsu, China..
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Effects of high-intensity interval training on gut microbiota profiles in 12 months' old ICR mice. J Physiol Biochem 2020; 76:539-548. [PMID: 32725451 DOI: 10.1007/s13105-020-00758-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 07/17/2020] [Indexed: 10/23/2022]
Abstract
High-intensity interval training (HIT) has been proposed to exert multiple beneficial effects and positively affect gut microbiota, while how HIT would affect gut microbiota profiles in middle-aged mice remain unreported. Male ICR mice (12 months old) were divided into two groups, i.e., control group (CON) and HIT exercise group (HIT) given HIT running with a total of 7 weeks. Fecal content from the gut was collected eventually and gut microbiota were determined via 16S rRNA gene sequencing. Compared with CON group, mice from HIT group exhibited improved gut microbial diversity including increased Shannon index. Compared with the CON group, at the phylum level, the relative abundance of Proteobacteria and TM7 was significantly decreased and increased, respectively, from HIT group. At the genera level, HIT group had significantly increased Dorea and Dehalobacterium, while decreased Candidatus Arthromitus. PICRUSt analysis at level 2 and level 3 of KEGG pathways demonstrated that the cecal microbiota of mice from HIT group had significantly enriched pathways involved in carbohydrate metabolism, signal transduction mechanisms, and transcription, while reduced pathways involved in renal cell carcinoma, Huntington's disease, pathways in cancer, various types of N-glycan biosynthesis, Alzheimer's disease, glycan biosynthesis and metabolism, lipopolysaccharide biosynthesis, cell motility and secretion, and lipopolysaccharide biosynthesis proteins. In conclusion, HIT could dynamically alter gut microbiota profiles in middle-aged mice. How altered gut microbiota profiles could affect the biological functions of HIT need to be further explored.
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Nemoto N, Takeda Y, Nara H, Araki A, Gazi MY, Takakubo Y, Naganuma Y, Takagi M, Asao H. Analysis of intestinal immunity and flora in a collagen-induced mouse arthritis model: differences during arthritis progression. Int Immunol 2020; 32:49-56. [PMID: 31562738 DOI: 10.1093/intimm/dxz058] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 08/28/2019] [Indexed: 12/29/2022] Open
Abstract
Intestinal immunity and flora are reported to be associated with the onset of rheumatoid arthritis. However, differences in the intestinal immunity and flora dynamics between the initial peak and relapse of arthritis have not been investigated. Here we analyzed the lymphocyte populations in different lymphoid tissues, the IgA in feces, and the intestinal flora at the initial peak and the relapse phase of arthritis in a collagen-induced arthritis (CIA) mouse model. In this model compared with the control group, the percentage of RORγt+CD4+ T cells in the mesenteric lymph nodes (mLN) was increased at the initial peak but decreased at the relapse stage of arthritis, and the opposite changes were observed in the spleen. The percentage of Foxp3+CD4+ T cells was unchanged at the initial peak in both tissues but increased only in the mLN at the relapse stage. The IgA in feces increased with the progression of arthritis, and bacterial analysis revealed that some specific bacterial families were changed at the peak and relapse stages of arthritis. Finally, the immune dynamics under different arthritic conditions were examined by integrating these factors using principal component analysis (PCA). PCA showed that the immunological and intestinal flora profiles were different between the initial peak and the relapse of the arthritis. Our findings suggest that the intestinal immunity and the environment change drastically with the progress of arthritis.
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Affiliation(s)
- Nobuhito Nemoto
- Department of Immunology, 2-2-2 Iidanishi, Yamagata city, Yamagata, Japan.,Department of Orthopaedic Surgery, Yamagata University Faculty of Medicine, 2-2-2 Iidanishi, Yamagata city, Yamagata, Japan
| | - Yuji Takeda
- Department of Immunology, 2-2-2 Iidanishi, Yamagata city, Yamagata, Japan
| | - Hidetoshi Nara
- Department of Immunology, 2-2-2 Iidanishi, Yamagata city, Yamagata, Japan
| | - Akemi Araki
- Department of Immunology, 2-2-2 Iidanishi, Yamagata city, Yamagata, Japan
| | - Md Yeashin Gazi
- Department of Immunology, 2-2-2 Iidanishi, Yamagata city, Yamagata, Japan
| | - Yuya Takakubo
- Department of Orthopaedic Surgery, Yamagata University Faculty of Medicine, 2-2-2 Iidanishi, Yamagata city, Yamagata, Japan
| | - Yasushi Naganuma
- Department of Orthopaedic Surgery, Yamagata University Faculty of Medicine, 2-2-2 Iidanishi, Yamagata city, Yamagata, Japan
| | - Michiaki Takagi
- Department of Orthopaedic Surgery, Yamagata University Faculty of Medicine, 2-2-2 Iidanishi, Yamagata city, Yamagata, Japan
| | - Hironobu Asao
- Department of Immunology, 2-2-2 Iidanishi, Yamagata city, Yamagata, Japan
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Kazakevych J, Denizot J, Liebert A, Portovedo M, Mosavie M, Jain P, Stellato C, Fraser C, Corrêa RO, Célestine M, Mattiuz R, Okkenhaug H, Miller JR, Vinolo MAR, Veldhoen M, Varga-Weisz P. Smarcad1 mediates microbiota-induced inflammation in mouse and coordinates gene expression in the intestinal epithelium. Genome Biol 2020; 21:64. [PMID: 32160911 PMCID: PMC7065452 DOI: 10.1186/s13059-020-01976-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 02/25/2020] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND How intestinal epithelial cells interact with the microbiota and how this is regulated at the gene expression level are critical questions. Smarcad1 is a conserved chromatin remodeling factor with a poorly understood tissue function. As this factor is highly expressed in the stem and proliferative zones of the intestinal epithelium, we explore its role in this tissue. RESULTS Specific deletion of Smarcad1 in the mouse intestinal epithelium leads to colitis resistance and substantial changes in gene expression, including a striking increase of expression of several genes linked to innate immunity. Absence of Smarcad1 leads to changes in chromatin accessibility and significant changes in histone H3K9me3 over many sites, including genes that are differentially regulated upon Smarcad1 deletion. We identify candidate members of the gut microbiome that elicit a Smarcad1-dependent colitis response, including members of the poorly understood TM7 phylum. CONCLUSIONS Our study sheds light onto the role of the chromatin remodeling machinery in intestinal epithelial cells in the colitis response and shows how a highly conserved chromatin remodeling factor has a distinct role in anti-microbial defense. This work highlights the importance of the intestinal epithelium in the colitis response and the potential of microbial species as pharmacological and probiotic targets in the context of inflammatory diseases.
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Affiliation(s)
- Juri Kazakevych
- Nuclear Dynamics, Babraham Institute, Cambridge, CB22 3AT, UK
| | - Jérémy Denizot
- Nuclear Dynamics, Babraham Institute, Cambridge, CB22 3AT, UK.,Present Address: Université Clermont Auvergne, Inserm U1071, INRA USC2018, M2iSH, F-63000, Clermont-Ferrand, France
| | - Anke Liebert
- Nuclear Dynamics, Babraham Institute, Cambridge, CB22 3AT, UK.,Present Address: The Francis Crick Institute, London, NW1 1AT, UK
| | - Mariana Portovedo
- Laboratory of Immunoinflammation, Institute of Biology, UNICAMP, Campinas, 13083-862, Brazil
| | - Mia Mosavie
- School of Biological Sciences, University of Essex, Colchester, CO4 3SQ, UK
| | - Payal Jain
- Nuclear Dynamics, Babraham Institute, Cambridge, CB22 3AT, UK
| | | | - Claire Fraser
- Nuclear Dynamics, Babraham Institute, Cambridge, CB22 3AT, UK
| | - Renan Oliveira Corrêa
- Laboratory of Immunoinflammation, Institute of Biology, UNICAMP, Campinas, 13083-862, Brazil
| | | | - Raphaël Mattiuz
- Nuclear Dynamics, Babraham Institute, Cambridge, CB22 3AT, UK
| | | | - J Ross Miller
- Nuclear Dynamics, Babraham Institute, Cambridge, CB22 3AT, UK
| | | | - Marc Veldhoen
- Lymphocyte Signalling and Development, Babraham Institute, Cambridge, CB22 3AT, UK.,Present Address: Instituto de Medicina Molecular
- Joâo Lobo Antunes, Faculdade de Medicina da Universidade de Lisboa, 1649-028, Lisbon, Portugal
| | - Patrick Varga-Weisz
- Nuclear Dynamics, Babraham Institute, Cambridge, CB22 3AT, UK. .,School of Biological Sciences, University of Essex, Colchester, CO4 3SQ, UK.
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Prabhu VR, Wasimuddin, Kamalakkannan R, Arjun MS, Nagarajan M. Consequences of Domestication on Gut Microbiome: A Comparative Study Between Wild Gaur and Domestic Mithun. Front Microbiol 2020; 11:133. [PMID: 32158434 PMCID: PMC7051944 DOI: 10.3389/fmicb.2020.00133] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2019] [Accepted: 01/21/2020] [Indexed: 12/12/2022] Open
Abstract
Although the gut microbiome benefits the host in several ways, how anthropogenic forces impact the gut microbiome of mammals is not yet completely known. Recent studies have noted reduced gut microbiome diversity in captive mammals due to changes in diet and living environment. However, no studies have been carried out to understand how the gut microbiome of wild mammals responds to domestication. We analyzed the gut microbiome of wild and captive gaur and domestic mithun (domestic form of gaur) to understand whether the gut microbiome exhibits sequential changes from wild to captivity and after domestication. Both captive and domestic populations were characterized by reduced microbial diversity and abundance as compared to their wild counterparts. Notably, two beneficial bacterial families, Ruminococcaceae and Lachnospiraceae, which are known to play vital roles in herbivores' digestion, exhibited lower abundance in captive and domestic populations. Consequently, the predicted bacterial functional pathways especially related to metabolism and immune system showed lower abundance in captive and domestic populations compared to wild population. Therefore, we suggest that domestication can impact the gut microbiome more severely than captivity, which might lead to adverse effects on host health and fitness. However, further investigations are required across a wide range of domesticates in order to understand the general trend of microbiome shifts in domestic animals.
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Affiliation(s)
- Vandana R. Prabhu
- Department of Genomic Science, School of Biological Sciences, Central University of Kerala, Kasaragod, India
| | - Wasimuddin
- Institute for Infectious Diseases, Faculty of Medicine, University of Bern, Bern, Switzerland
| | - Ranganathan Kamalakkannan
- Department of Genomic Science, School of Biological Sciences, Central University of Kerala, Kasaragod, India
| | - Moolamkudy Suresh Arjun
- Department of Genomic Science, School of Biological Sciences, Central University of Kerala, Kasaragod, India
| | - Muniyandi Nagarajan
- Department of Genomic Science, School of Biological Sciences, Central University of Kerala, Kasaragod, India
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